Variant classification summary

NM_000551.3:c.154G>A

VHL · NP_000542.1:p.(Glu52Lys) · NM_000551.3

GRCh37: chr3:10183685 G>A · GRCh38: chr3:10142001 G>A

Gene: VHL Transcript: NM_000551.3

Final call

Benign

BA1 stand-alone benign BS1 strong benign BP4 supporting benign BP6 supporting benign

Variant details

Gene

VHL

Transcript

NM_000551.3

Protein

NP_000542.1:p.(Glu52Lys)

gnomAD AF

6.75855778693236e-05 (v4.1)

ClinVar

Benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000551.3:c.154G>A (p.Glu52Lys) has a GroupMax filtering allele frequency of 0.08611% (0.0008611) in gnomAD v4.1, which exceeds the VHL VCEP BA1 stand-alone benign threshold of 0.0156% (0.000156).

2

The variant is observed in 107 of 1,583,178 alleles in gnomAD v4.1, including 1 homozygote, with highest frequency in the African/African American population (78/74,388 alleles, 0.1049%).

3

BA1 as stand-alone benign is independently sufficient to classify the variant as Benign regardless of other evidence criteria.

4

BS1 is also met at strong benign level: gnomAD v4 GroupMax FAF 0.0008611 exceeds the VCEP BS1 threshold of 0.0000156.

5

BP4 is met at supporting benign level: SpliceAI predicts no splicing impact (max delta = 0.00).

6

The variant was observed in 1-2 VHL families (Olschwang 1998, Gallou 2004) but this does not meet PS4 thresholds and is outweighed by population frequency data.

7

ClinVar expert panel (ClinGen VHL VCEP) classifies this variant as Benign (VCV000161402).

8

REVEL score of 0.559 does not meet the VHL VCEP PP3 threshold of ≥0.664. BayesDel score of -0.059 is consistent with a benign prediction.

9

The variant alters codon 52, which is upstream of the second VHL initiation codon (Met54); only pVHL30 is affected while pVHL19 remains intact. This N-terminal region is outside recognized VHL critical functional domains.

Final determination: Rule17 in the ClinGen VHL Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VHL Version 1.1.0 v1.1.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Benign.

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 applies only to null variants (nonsense, frameshift, canonical splice). NM_000551.3:c.154G>A is a missense variant (p.Glu52Lys) and does not fall into any PVS1 null-variant bucket. Additionally, the variant is upstream of the second initiation codon (Met54) and alters only pVHL30, not pVHL19.
PS1	Not met	PS1 requires a different nucleotide change at the same codon previously classified as pathogenic by the VHL VCEP. No VCEP-interpreted pathogenic variant at codon 52 with a different nucleotide change was identified. E52K itself is the variant under assessment; no comparator missense at codon 52 (e.g., E52Q, E52X) has been established as pathogenic under VCEP specifications.
PS2	Not met	No de novo occurrence with confirmed maternity and paternity was identified for this variant in the reviewed literature or ClinVar submissions.
PS3	Not met	No validated in vitro or in vivo functional assay demonstrating a damaging effect of E52K on VHL protein function (HIF1/2a degradation, VBC complex stability, or ECM/fibronectin binding). Computational modeling in PMID:26211615 suggests E52K may alter pVHL-N conformation, but this is in silico prediction and does not meet the Brnich et al. framework for PS3 functional evidence.
PS4	Not met	The variant has been reported in a small number of VHL probands: one type 1 VHL patient in Olschwang et al. (1998, family V285) and one family (285a) in Gallou et al. (2004) with renal involvement. This level of proband evidence (approximately 1-2 probands) falls far below even the PS4_Supporting threshold of 1 point under the VHL VCEP proband scoring tables. Additionally, the variant is present in gnomAD at appreciable frequency, further weakening any case-control argument.	PMID:9829912 PMID:15300849
PS5	Not met	No reputable source reports this variant as pathogenic. ClinVar classifies it as Benign by the ClinGen VHL Variant Curation Expert Panel (expert panel review). The majority of clinical laboratory submissions are Uncertain Significance (6) or Likely benign/Benign (6).	clinvar
PM1	Not met	Codon 52 resides in the pVHL N-terminal acidic repeat region (AA 1-53), upstream of the second initiation codon (Met54). This region is not a recognized VHL germline hotspot or critical functional domain (Beta domain: AA 63-154, Alpha domain: AA 155-192, Second Beta: AA 193-204). COSMIC reports only 1 somatic instance at this residue, well below the 10-instance threshold for PM1_Moderate.	cspec
PM2	Not met	VHL VCEP PM2_Supporting requires GroupMax FAF ≤ 0.00000156 (0.000156%) in gnomAD v4. This variant has gnomAD v4 GroupMax FAF = 0.0008611 (0.08611%), which is approximately 552-fold above the PM2 threshold. The variant is also present in gnomAD v2.1 (19 alleles, grpmax FAF 0.00037662).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	PM5 requires a different missense change at the same residue previously classified as pathogenic by the VHL VCEP. No alternative missense variant at codon 52 (e.g., E52Q, E52D, E52X) has been reported and classified as pathogenic under VCEP specifications. The pm5_candidates search found no eligible comparator variants.
PM6	Not met	No assumed de novo occurrence without maternity/paternity confirmation was identified for this variant in the reviewed literature or ClinVar submissions.
PP1	Not met	No co-segregation data meeting VHL VCEP thresholds was identified. The Olschwang et al. (1998) report includes 1 affected/1 unaffected family member tested, which provides no meiosis count toward PP1 thresholds (minimum 3-4 meioses for supporting).	PMID:9829912
PP2	N/A	VHL VCEP explicitly states PP2 is not applicable. gnomAD shows VHL is not intolerant to missense variation (Z score = -0.39); benign missense variants exist in VHL.	cspec
PP3	Not met	VHL VCEP PP3 for missense variants requires REVEL score ≥ 0.664. This variant has REVEL = 0.559, which falls below the threshold. BayesDel score = -0.059 (benign-leaning). SpliceAI max delta = 0.00 (no predicted splicing impact), so PP3 for splicing is also not applicable.	revel bayesdel spliceai cspec
PP4	N/A	VHL VCEP states PP4 is not applicable; combined with PS4 to avoid double counting probands.	cspec
PP5	N/A	VHL VCEP states PP5 is not applicable. Criterion not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Met	VHL VCEP BA1 threshold: GroupMax FAF ≥ 0.000156 (0.0156%) in gnomAD v4. This variant has gnomAD v4 GroupMax FAF = 0.0008611 (0.08611%) in the African/African American population (78/74,388 alleles, 1 homozygote). This is approximately 5.5-fold above the BA1 cutoff. The variant is also observed in gnomAD v2.1 with grpmax FAF 0.00037662 in the same population group. BA1 is met as stand-alone benign evidence, independently sufficient to classify this variant as benign regardless of other criteria.	gnomad_v4 gnomad_v2 cspec
BS1	Met	VHL VCEP BS1 threshold: GroupMax FAF ≥ 0.0000156 (0.00156%) in gnomAD v4. This variant has gnomAD v4 GroupMax FAF = 0.0008611 (0.08611%), which is approximately 55-fold above the BS1 cutoff. BS1 is met as strong benign evidence. Note: BA1 (stand-alone) subsumes BS1; both are independently met.	gnomad_v4 cspec
BS2	Not met	VHL VCEP BS2 requires at least 3 individuals ≥65 years old, unaffected, harboring this variant. While gnomAD v4 reports 1 homozygote and 107 total alleles, no clinical phenotype data on unaffected status of these population individuals is available. The criteria-specific clinical data for BS2 (age, full phenotyping, VHL cancer screening) are not available from population databases alone.	gnomad_v4
BS3	Not met	No validated functional assay demonstrating benign effect (WT-like function) of E52K on HIF1/2a degradation, VBC complex stability, or ECM/fibronectin binding. The variant is located upstream of the Met54 second initiation codon and does not affect pVHL19, which retains full tumor suppressor function; however, no direct experimental evidence confirming benign functional effect of E52K was identified.
BS4	Not met	No lack-of-segregation data available. The Olschwang et al. (1998) family V285 has 1 affected/0 unaffected carriers, providing no segregation information for BS4. No multi-family segregation data was identified.
BP1	N/A	VHL VCEP states BP1 is not applicable. Truncating variants account for only a portion of disease-causing variants in VHL; missense variants are a well-established mechanism of disease.	cspec
BP2	Not met	BP2_Strong would apply if the variant were observed in the homozygous state in an individual without VHL disease or congenital polycythemia. gnomAD v4 reports 1 homozygous individual, but no clinical phenotype data are available to confirm absence of VHL-related disease or congenital polycythemia. Without confirmatory clinical data, BP2 cannot be applied.	gnomad_v4
BP3	N/A	Pre-skipped: substitution variant, BP3 applies to in-frame indels in repetitive regions.
BP4	Met	VHL VCEP BP4: missense predictors should not be used for BP4, but BP4 can be applied to assess lack of splicing impact with SpliceAI ≤ 0.1 and VarSeak Class 1 or 2. This variant has SpliceAI max delta = 0.00, indicating no predicted splice impact. Per VCEP instructions, the SpliceAI score alone can be applied if VarSeak is unable to accept the variant type. The variant is a coding missense with no predicted effect on splicing.	spliceai cspec
BP5	Not met	BP5 requires two or more co-occurrences with pathogenic variants in a different gene that fully explain the patient's phenotype, with specific phenotype non-overlap criteria. No such co-occurrence evidence was identified for this variant.
BP6	Met	Expert panel ClinGen VHL Variant Curation Expert Panel, ClinGen classified as Benign.	cspec clinvar
BP7	N/A	BP7 applies only to silent (synonymous) or intronic variants with no predicted splice impact and PhyloP ≤ 0.2. This variant is a missense substitution (p.Glu52Lys), not a silent or intronic variant.	cspec

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