NM_058216.2:c.145+1G>A

RAD51C · NP_478123.1:p.? · NM_058216.2

GRCh37: chr17:56770150 G>A · GRCh38: chr17:58692789 G>A

Gene: RAD51C Transcript: NM_058216.2

Final call

Pathogenic

PVS1 very strong PS3 supporting PM2 moderate

Variant details

Gene

RAD51C

Transcript

NM_058216.2

Protein

NP_478123.1:p.?

gnomAD AF

6.195042231602893e-07 (v4.1)

ClinVar

Likely pathogenic

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_058216.2:c.145+1G>A is a canonical splice donor variant affecting the invariant +1 position of RAD51C intron 1, predicted to abolish normal splicing (SpliceAI delta 0.86). PVS1 is applied at very strong strength.

Functional studies of c.145+1G>T, a different nucleotide substitution at the same canonical +1 position, demonstrated complete inactivation of the 5' splice site in a minigene splicing reporter assay and loss of normal RAD51C transcript expression in patient leukocytes (Meindl et al., 2010). PS3 is applied at supporting strength.

This variant is extremely rare in population databases: gnomAD v2.1 AF = 3.98e-6 (1/251,282 alleles) and v4.1 AF = 6.20e-7 (1/1,614,194 alleles), with no homozygotes observed. PM2 is applied at moderate strength.

This variant has been reported in ClinVar (Variation ID 484741) as Likely pathogenic by four clinical laboratories and Pathogenic by one clinical laboratory, with review status of criteria provided, single submitter.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Pathogenic classification based on the observed combination of very strong, strong, moderate, and supporting pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	NM_058216.2:c.145+1G>A is a canonical splice donor variant affecting the +1 position of intron 1, disrupting the invariant GT dinucleotide. RAD51C loss of function is an established disease mechanism for autosomal dominant hereditary breast and ovarian cancer and autosomal recessive Fanconi anemia. SpliceAI predicts a strong splice-altering effect (max delta score 0.86). The variant is predicted to abolish normal RAD51C transcript expression, consistent with experimental data showing complete inactivation of the 5' splice site when the same canonical position is disrupted by a different nucleotide substitution (c.145+1G>T evaluated in Meindl et al. 2010). PVS1 is applied at very strong strength under the generic ACMG/ClinGen SVI PVS1 framework (PMC6185798).	pvs1_variant_assessment pvs1_gene_context spliceai PMID:20400964
PS1	N/A	PS1 applies to missense variants with a different amino acid change at the same residue as a known pathogenic missense variant. This is a canonical splice site variant, not a missense substitution.
PS2	Not met	No de novo occurrence data is available for this variant. No published report of a confirmed de novo observation was identified in the literature or ClinVar submissions.
PS3	Met	Meindl et al. (2010, PMID:20400964) experimentally characterized c.145+1G>T, a different nucleotide substitution at the same canonical +1 splice donor position. RT-PCR of patient leukocytes showed reduced normal RAD51C-001 transcript and increased nonfunctional RAD51C-008 transcript. A minigene splicing reporter assay in HeLa cells demonstrated complete inactivation of the mutant 5' splice site. LOH of the wild-type allele was confirmed in tumor tissue. Although the exact variant (G>A) was not directly tested, both G>T and G>A disrupt the invariant GT dinucleotide at the canonical +1 position, and the mechanism of splice disruption is identical. Supporting strength is applied because the exact variant was not tested but functional data on the same position strongly supports a deleterious splice effect.	PMID:20400964
PS4	Not met	No case-control study with statistical significance has been published for NM_058216.2:c.145+1G>A specifically. The variant is present in ClinVar with 5 clinical laboratory submissions (4 Likely pathogenic, 1 Pathogenic), but these do not constitute a controlled case-control comparison. The Meindl et al. study reported c.145+1G>T (not G>A) in 1 of 480 BC/OC pedigrees.	clinvar
PS5	N/A	PS5 applies to the same variant identified in multiple patients with a specific phenotype. This criterion was not included in the assess list.
PM1	Not met	The variant is a canonical splice donor site at the exon 1/intron 1 boundary. No specific mutational hotspot or well-characterized critical functional domain has been identified at this splice junction position. The variant disrupts splicing rather than targeting a defined protein domain. Cancerhotspots.org does not list this position as a significant residue.
PM2	Met	This variant is extremely rare in population databases. gnomAD v2.1 reports an allele frequency of 3.98e-6 (1/251,282 alleles, 0 homozygotes) and gnomAD v4.1 reports an allele frequency of 6.20e-7 (1/1,614,194 alleles, 0 homozygotes). Both are well below the PM2 threshold of <0.1%. The highest subpopulation frequency is in East Asian populations (v2.1: 5.44e-5; v4.1: 2.23e-5).	gnomad_v2 gnomad_v4
PM5	N/A	PM5 applies to missense variants where a different pathogenic missense change has been identified at the same amino acid residue. This is a canonical splice site variant (c.145+1G>A), not a missense substitution. No same-residue missense comparator can be identified from the variant consequence.
PM6	Not met	No de novo occurrence has been reported for this variant. PM6 requires a confirmed de novo observation with both maternity and paternity confirmed. No such data was identified in ClinVar submissions or the reviewed literature.
PP1	Not met	No segregation data is available for NM_058216.2:c.145+1G>A. Meindl et al. (2010) reported segregation of c.145+1G>T in one family (three sisters with breast/ovarian cancer), but this is a different nucleotide substitution. No segregation analysis has been published for c.145+1G>A specifically.	PMID:20400964
PP2	N/A	PP2 applies when a missense variant occurs in a gene with a low rate of benign missense variation and where missense variants are a common disease mechanism. This is a canonical splice site variant, not a missense substitution.
PP3	Not met	While SpliceAI (max delta 0.86) and BayesDel (0.66) predict a deleterious effect, the splice prediction evidence is already captured by PVS1 for this canonical splice variant. Under ClinGen SVI PVS1 recommendations (PMC6185798) and standard ACMG/AMP practice, PP3 should not be double-counted for the same splice-effect prediction evidence that supports PVS1. PP3 is therefore not applied to avoid evidence stacking.	spliceai bayesdel
PP4	Not met	No patient phenotype or family history data is available for adjudication. The variant is reported in ClinVar as Likely pathogenic/Pathogenic by clinical testing laboratories, but specific phenotype details are not provided in the available data. PP4 requires that the patient's phenotype or family history is highly specific for the disease associated with the gene.	clinvar
PP5	Not met	PP5 requires a reputable source (e.g., ClinGen expert panel, 3-star ClinVar review status) to have classified the variant as pathogenic. The ClinVar record (Variation ID 484741) has review status 'criteria provided, single submitter' (1-star), consisting of 5 individual clinical laboratory submissions. No expert panel review has been performed. Under the adjudication rule, PP5 is applied at supporting strength only when ClinVar review status is 3-star expert panel, which is not met here.	clinvar
BA1	Not met	The allele frequency in gnomAD is well below the BA1 threshold of >1%. gnomAD v2.1 AF = 3.98e-6 (0.0004%) and v4.1 AF = 6.20e-7 (0.00006%). This variant is extremely rare, not common.	gnomad_v2 gnomad_v4
BS1	Not met	The allele frequency in gnomAD is well below the BS1 threshold of >0.3%. gnomAD v2.1 AF = 3.98e-6 (0.0004%) and v4.1 AF = 6.20e-7 (0.00006%). The variant is significantly rarer than expected for a benign polymorphism.	gnomad_v2 gnomad_v4
BS2	Not met	No data is available showing this variant observed in healthy adults with full penetrance expected. The single gnomAD observation (East Asian, v2.1 exomes) lacks clinical phenotype confirmation and penetrance data. BS2 requires observation in a healthy adult individual where the disease is fully penetrant at an early age, which cannot be confirmed from population database allele counts alone.
BS3	Not met	BS3 requires well-established in vitro or in vivo functional studies showing no damaging effect on protein function or splicing. The available functional data for the same splice position (c.145+1G>T in Meindl et al. 2010) demonstrates a damaging effect: complete inactivation of the 5' splice site, reduced normal transcript, and LOH in tumor tissue. The evidence points toward a deleterious effect rather than a benign one.	PMID:20400964
BS4	Not met	No segregation data is available for NM_058216.2:c.145+1G>A showing lack of co-segregation with disease. The only published segregation data involves c.145+1G>T (Meindl et al. 2010) which showed co-segregation with disease, not lack of segregation.	PMID:20400964
BP1	N/A	BP1 applies when a missense variant occurs in a gene where truncating variants are a known disease mechanism and only truncating variants are pathogenic. This is a canonical splice site variant, not a missense substitution.
BP2	Not met	No data available showing this variant observed in trans with a known pathogenic variant or in cis with a pathogenic variant in a recessive disorder. RAD51C has both autosomal dominant (HBOC) and autosomal recessive (Fanconi anemia) inheritance patterns, but no phase data is available for this variant.
PM3	N/A	PM3 applies to variants observed in trans with a pathogenic variant in a recessive disorder. No phase data available; assessed as trivially not_applicable per adjudication instructions.
PM4	N/A	PM4 applies to protein length changes due to in-frame deletions/insertions or stop-loss variants. This is a single nucleotide substitution at a canonical splice site.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without a known function. This is a single nucleotide substitution at a canonical splice site.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product. Both SpliceAI (max delta 0.86) and BayesDel (0.66) predict a deleterious effect. The in silico evidence suggests a damaging impact on splicing, not a benign one.	spliceai bayesdel
BP5	Not met	No data available showing this variant found in a case with an alternative molecular basis for disease. BP5 requires observation in an individual with a clear alternate genetic cause for their phenotype.
BP6	Not met	BP6 requires a reputable source (3-star ClinVar expert panel) to have classified the variant as benign or likely benign. The ClinVar record (Variation ID 484741) shows Likely pathogenic/Pathogenic classifications from clinical laboratories. No benign classification exists from any source.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants with no predicted impact on splicing. This is a canonical +1 splice donor variant with strong SpliceAI prediction (delta 0.86), which is definitively predicted to alter splicing.

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