Variant classification summary

NM_002524.4:c.291-8G>A

NRAS · NP_002515.1:p.? · NM_002524.4

GRCh37: chr1:115252357 C>T · GRCh38: chr1:114709736 C>T

Gene: NRAS Transcript: NM_002524.4

Final call

VUS

BP4 supporting benign BP6 supporting benign BP7 supporting benign

Variant details

Gene

NRAS

Transcript

NM_002524.4

Protein

NP_002515.1:p.?

gnomAD AF

0.0001038934538414449 (v4.1)

ClinVar

Likely Benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_002524.4:c.291-8G>A is an intronic variant in NRAS (intron 2, c.291-8).

2

The ClinGen RASopathy Expert Panel VCEP v2.3.0 was applied as the primary classification framework.

3

No pathogenic criteria were met. PVS1, PS1, PS5, PM1, PM5, PP2, PP4, PP5, BS3, BP1, BP3, BP6, PM3, and PM4 are not applicable to this intronic variant per VCEP specifications.

4

Two benign supporting criteria are met: BP4 (SpliceAI predicts no splicing impact; max delta 0.01; predicted outcome does not match gain-of-function disease mechanism) and BP7 (intronic variant at non-canonical position with no predicted splice effect).

5

The variant is present in gnomAD at low frequency: v2.1 AF=0.0064% (18/282,784 alleles), v4.1 AF=0.010% (167/1,607,416 alleles, 1 homozygote). These frequencies do not reach VCEP thresholds for BA1 (>=0.05%) or BS1 (>=0.025%), but the presence in population databases precludes PM2 (which requires absence from gnomAD).

6

No de novo occurrences, functional studies, cosegregation data, or case-control enrichment have been reported for this variant in ClinVar or the published literature.

7

Per VCEP Rule 19, >=2 supporting benign criteria (BP4 + BP7) classifies this variant as Likely Benign.

8

This classification is concordant with the ClinGen RASopathy VCEP expert panel assessment of Likely Benign (ClinVar Variation ID 44575).

Final determination: No criteria-combination rule matched the adjudicated criteria in the ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.3.0 v2.3.0 framework, so the variant remains a Variant of Uncertain Significance pending human review.

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	N/A	PVS1 is marked Not Applicable by the ClinGen RASopathy VCEP v2.3.0. Additionally, this intronic variant (c.291-8G>A) does not fall into the generic PVS1 null-variant buckets (nonsense, frameshift, or canonical +/-1,2 splice consensus).	cspec pvs1_generic_framework
PS1	N/A	PS1 requires the same amino acid change as a previously established pathogenic variant. c.291-8G>A is an intronic variant with no amino acid consequence (p.?), so PS1 cannot be applied.	cspec
PS2	Not met	No de novo occurrence with confirmed maternity and paternity has been reported for NM_002524.4:c.291-8G>A in ClinVar submissions or the published literature.	clinvar
PS3	Not met	No functional studies from the VCEP-approved assay list (RAS activation, MEK/ERK activation assays) have been performed on c.291-8G>A. SpliceAI predicts no splicing impact (max delta 0.01), consistent with no functional consequence.	cspec spliceai
PS4	Not met	The variant is present in gnomAD at 167/1,607,416 alleles (v4.1, AF=0.010%), including one homozygote. This population frequency argues against significant enrichment in RASopathy cases. No case-control study demonstrates case enrichment.	gnomad_v2 gnomad_v4
PS5	N/A	PS5 requires the same nucleotide change as a previously established pathogenic variant. c.291-8G>A is a deep intronic substitution; no pathogenic variant has been established at this same nucleotide position.	cspec
PM1	N/A	VCEP PM1 applies only to critical functional domains defined in the supplementary table (P-loop AA 10-17, SW1 AA 25-40, SW2 AA 57-64, SAK AA 145-156). c.291-8G>A is located in intron 2, far outside all defined functional domains.	cspec vcep_alignment_with_pm1_domains_pptx
PM2	Not met	VCEP PM2 requires the variant be absent from gnomAD. c.291-8G>A is present in gnomAD v2.1 (18/282,784 alleles, AF=0.0064%) and v4.1 (167/1,607,416 alleles, AF=0.010%), including one homozygous individual.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a missense change at a residue with a previously established (likely) pathogenic missense variant. c.291-8G>A is an intronic variant with no protein consequence; pm5_candidates confirms the variant class is not missense-like.	cspec pm5_candidates
PM6	Not met	No assumed de novo observation (without confirmed parentage) has been reported for this variant in ClinVar or the literature.	clinvar
PP1	Not met	No cosegregation data with disease in multiple affected family members has been reported for c.291-8G>A. The VCEP requires >=3 informative meioses for Supporting strength.
PP2	N/A	VCEP explicitly marks PP2 as Not Applicable because the missense z-score for NRAS is <3.09 in gnomAD.	cspec
PP3	Not met	SpliceAI predicts no splicing impact (max delta score = 0.01), which does not support a deleterious effect. The VCEP PP3 rule for splicing impact requires the predicted outcome to match the gain-of-function disease mechanism, which is not satisfied.	spliceai cspec
PP4	N/A	VCEP explicitly marks PP4 as Not Applicable for this VCEP (see PS4 instead).	cspec
PP5	N/A	VCEP explicitly marks PP5 as Not Applicable for this VCEP, per ClinGen SVI VCEP Review Committee recommendation.	cspec
BA1	Not met	VCEP BA1 requires gnomAD filtering allele frequency >= 0.05%. gnomAD v2.1 grpmax FAF = 0.0047% and v4.1 grpmax FAF = 0.010%, both well below the 0.05% threshold.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	VCEP BS1 requires gnomAD filtering allele frequency >= 0.025%. gnomAD v2.1 grpmax FAF = 0.0047% and v4.1 grpmax FAF = 0.010%, both below the 0.025% threshold.	gnomad_v2 gnomad_v4 cspec
BS2	Not met	No observation of this variant in a healthy adult individual (homozygous or heterozygous) with documented unaffected clinical status has been reported. gnomAD homozygote count alone is insufficient without phenotype data.	gnomad_v4
BS3	N/A	VCEP explicitly marks BS3 as Not Applicable for this VCEP.	cspec
BS4	Not met	No published data demonstrate lack of segregation of c.291-8G>A in affected members of a family. The VCEP requires only one informative meiosis, but none are documented.
BP1	N/A	VCEP BP1 applies only to truncating variants (nonsense, frameshift, canonical splice sites, initiation codon, entire gene or multi-exon deletion). c.291-8G>A is a deep intronic substitution and is not truncating.	cspec
BP2	Not met	No evidence of c.291-8G>A observed in trans with a known pathogenic NRAS variant, or as an alternative molecular cause for a RASopathy phenotype.
BP4	Met	SpliceAI predicts no splicing impact (max delta score = 0.01). The predicted splicing outcome is negligible and does not support a gain-of-function disease mechanism for RASopathies. Per VCEP BP4 instructions, this criterion is applicable for splicing variants where the predicted outcome is negligible or does not match the disease mechanism.	spliceai cspec
BP5	Not met	No alternative molecular cause for a RASopathy has been identified in cases carrying c.291-8G>A.
BP6	Met	Expert panel ClinGen RASopathy Variant Curation Expert Panel classified as Likely benign.	cspec clinvar
BP7	Met	c.291-8G>A is an intronic variant at position -8 from exon 3 (not a canonical splice site). SpliceAI predicts no impact to the splice consensus sequence nor the creation of a new splice site (max delta = 0.01). Per VCEP BP7, this rule is applicable for intronic positions except canonical splice sites and should be used in conjunction with BP4.	spliceai cspec

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