NM_002775.4:c.333G>A

HTRA1 · NP_002766.1:p.(Val111=) · NM_002775.4

GRCh37: chr10:124221501 G>A · GRCh38: chr10:122461985 G>A

Gene: HTRA1 Transcript: NM_002775.4

Final call

VUS

PM2 supporting BP4 supporting benign BP7 supporting benign

Variant details

Gene

HTRA1

Transcript

NM_002775.4

Protein

NP_002766.1:p.(Val111=)

gnomAD AF

6.559940803094193e-07 (v4.1)

ClinVar

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_002775.4:c.333G>A (p.Val111=) is a synonymous variant in exon 1 of HTRA1, encoding HtrA serine peptidase 1.

This variant is ultra-rare in population databases: absent from gnomAD v2.1 and present in gnomAD v4.1 at an allele frequency of 6.56e-7 (1/1,524,404 alleles), satisfying PM2 at supporting strength.

Computational evidence supports a benign interpretation: REVEL score is 0.041 (well below the 0.5 pathogenic threshold), and SpliceAI predicts no splicing alteration (max delta = 0.00), meeting BP4 at supporting benign strength.

As a synonymous variant with no predicted splicing impact (SpliceAI max delta = 0.00) and low nucleotide conservation (REVEL = 0.041), this variant meets BP7 at supporting benign strength.

No functional studies, segregation data, de novo observations, case-control analyses, ClinVar classifications, or variant-specific publications are available for this variant. All other ACMG/AMP criteria are either not met or not applicable.

The evidence profile is conflicting: PM2_Supporting on the pathogenic side versus BP4_Supporting and BP7_Supporting on the benign side. Per the generic ACMG/AMP 2015 final classification rules (PMID:25741868), this constellation of conflicting supporting-level evidence is insufficient to reach a Likely Benign or Likely Pathogenic classification. The variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: Generic ACMG/AMP 2015 fallback rules identified both pathogenic and benign evidence, so the overall classification remains Variant of Uncertain Significance because the evidence is conflicting.

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 not applicable: NM_002775.4:c.333G>A is a synonymous variant (p.Val111=) that does not introduce a premature termination codon, disrupt a canonical splice site, or trigger nonsense-mediated decay. The variant falls into the 'other' bucket per ClinGen SVI PVS1 decision tree (PMC6185798) and is ineligible for generic PVS1 null-variant assessment.	pvs1_generic_framework pvs1_variant_assessment
PS1	N/A	PS1 requires the same amino acid change as a previously established pathogenic variant. This synonymous variant (p.Val111=) does not alter the amino acid sequence; there is no amino acid change to compare against a known pathogenic variant.
PS2	Not met	PS2 (de novo with confirmed paternity/maternity) is not met. No de novo observation of NM_002775.4:c.333G>A has been identified in ClinVar, the literature, or any evidence source in this case.
PS3	Not met	PS3 (well-established functional studies supporting a damaging effect) is not met. No functional assay data for NM_002775.4:c.333G>A was identified in ClinVar, the literature, or curated databases. OncoKB contains no functional annotation for this variant.
PS4	Not met	PS4 (prevalence in affected individuals significantly increased compared to controls) is not met. No case-control or cohort prevalence data for NM_002775.4:c.333G>A were identified. The variant is absent from ClinVar and no affected probands have been reported.
PS5	N/A	PS5 is not a standard ACMG/AMP 2015 criterion and is not defined in the generic ACMG framework applied here (PMID:25741868). No evidence supports invoking this criterion under any expanded framework.
PM1	Not met	PM1 (located in a mutational hot spot or critical functional domain) is not met. Residue V111 does not lie in a statistically significant cancer hotspot, and no critical functional domain enrichment for pathogenic HTRA1 variants at this position has been established.
PM2	Met	PM2 (absent or extremely low frequency in population databases) is met at supporting strength. NM_002775.4:c.333G>A is absent from gnomAD v2.1 and is present in gnomAD v4.1 at an allele frequency of 6.56e-7 (1/1,524,404 alleles), well below the generic ACMG PM2 threshold of 0.1%. It is also absent from gnomAD-Canada v1.0.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a novel missense variant at the same residue as a pathogenic missense variant. NM_002775.4:c.333G>A is a synonymous variant (p.Val111=), not a missense change. PM5 candidate harvesting could not identify valid same-residue comparators.	pm5_candidates
PM6	Not met	PM6 (de novo without confirmation of paternity/maternity) is not met. No de novo observation of NM_002775.4:c.333G>A has been reported in ClinVar or any literature source.
PP1	Not met	PP1 (cosegregation with disease in multiple affected family members) is not met. No family segregation data for NM_002775.4:c.333G>A has been reported.
PP2	N/A	PP2 applies specifically to missense variants in genes where missense variants are a common disease mechanism and benign missense variation is rare. NM_002775.4:c.333G>A is a synonymous variant (p.Val111=), not a missense change. PP2 is not applicable.
PP3	Not met	PP3 (multiple lines of computational evidence support a deleterious effect) is not met. REVEL score is 0.041 (benign-leaning; typical pathogenic threshold is >0.5). SpliceAI max delta score is 0.00 (no predicted splice impact). BayesDel score is unavailable. In silico evidence does not support pathogenicity.	revel spliceai
PP4	Not met	PP4 (patient phenotype or family history highly specific for the gene) is not met. No clinical phenotype data for individuals carrying NM_002775.4:c.333G>A is available in any evidence source.
PP5	Not met	PP5 (reputable source reports variant as pathogenic) is not met. NM_002775.4:c.333G>A is absent from ClinVar; no submitter has classified this variant. No publication reports it as pathogenic.	clinvar
BA1	Not met	BA1 (allele frequency >1% in any population) is not met. The highest observed subpopulation frequency is in the Admixed American population at 0.00198% (1/50,538 alleles), far below the 1% threshold.	gnomad_v4
BS1	Not met	BS1 (allele frequency greater than expected for the disorder) is not met. The total allele frequency in gnomAD v4.1 is 6.56e-7 (0.0000656%), well below the generic ACMG BS1 threshold of 0.3%.	gnomad_v4
BS2	Not met	BS2 (observed in a healthy adult individual in the homozygous state, or hemizygous in a male for an X-linked gene with full penetrance expected at an early age) is not met. No homozygotes for NM_002775.4:c.333G>A are reported in gnomAD.	gnomad_v4
BS3	Not met	BS3 (well-established functional studies show no damaging effect) is not met. No functional assay data for NM_002775.4:c.333G>A were identified. While REVEL and SpliceAI scores are consistent with a benign effect, these are in silico predictors and do not constitute well-established functional evidence.
BS4	Not met	BS4 (lack of segregation with disease in affected family members) is not met. No family segregation data for NM_002775.4:c.333G>A is available.
BP1	N/A	BP1 applies specifically to missense variants in genes where primarily truncating variants cause disease. NM_002775.4:c.333G>A is a synonymous variant (p.Val111=), not a missense change. BP1 is not applicable.
BP2	Not met	BP2 (observed in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant) is not met. No phase data or co-occurrence observations for NM_002775.4:c.333G>A with other HTRA1 variants are available.
BP4	Met	BP4 (multiple lines of computational evidence suggest no impact on gene product) is met at supporting benign strength. REVEL score is 0.041, strongly favoring a benign interpretation (typical pathogenic threshold >0.5). SpliceAI max delta score is 0.00, predicting no splicing alteration. Together these indicate no computational evidence of a deleterious effect.	revel spliceai
BP5	Not met	BP5 (variant found in a case with an alternate molecular basis for disease) is not met. No observation of NM_002775.4:c.333G>A in trans with, or co-occurring with, an alternate causative variant has been reported.
BP6	Not met	BP6 (reputable source reports variant as benign) is not met. NM_002775.4:c.333G>A is absent from ClinVar; no submitter has classified this variant as benign or likely benign.	clinvar
BP7	Met	BP7 (synonymous variant with no predicted splicing impact and nucleotide not highly conserved) is met at supporting benign strength. NM_002775.4:c.333G>A is a synonymous variant (p.Val111=). SpliceAI predicts no splicing alteration (max delta = 0.00). The low REVEL score (0.041) indicates the nucleotide position is not highly conserved across species.	spliceai revel

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