The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000551.4(VHL):c.341-2A>G

CA357004

223194 (ClinVar)

Gene: VHL
Condition: von Hippel-Lindau disease
Inheritance Mode: Autosomal dominant inheritance
UUID: 1f014c42-0db4-465a-9551-85c43c805797
Approved on: 2024-06-25
Published on: 2024-06-25

HGVS expressions

NM_000551.4:c.341-2A>G
NM_000551.4(VHL):c.341-2A>G
NC_000003.12:g.10146512A>G
CM000665.2:g.10146512A>G
NC_000003.11:g.10188196A>G
CM000665.1:g.10188196A>G
NC_000003.10:g.10163196A>G
NG_008212.3:g.9878A>G
ENST00000696142.1:c.*18-2A>G
ENST00000696143.1:c.600-3275A>G
ENST00000696153.1:c.341-2A>G
ENST00000256474.3:c.341-2A>G
ENST00000256474.2:c.341-2A>G
ENST00000345392.2:c.341-3275A>G
ENST00000477538.1:n.477-2A>G
NM_000551.3:c.341-2A>G
NM_198156.2:c.341-3275A>G
NM_001354723.1:c.*18-3275A>G
NM_001354723.2:c.*18-3275A>G
NM_198156.3:c.341-3275A>G
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Pathogenic

Met criteria codes 3
PVS1 PS4_Moderate PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen VHL Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VHL Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
VHL VCEP
The variant NM_000551.3(VHL):c.341-2A>G is a canonical splice site within the 1st intron of the VHL gene, and is predicted to undergo nonsense mediated decay (PVS1). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). This variant has been reported in at least 3 studies, in cases or families with VHL syndrome or VHL-related cancers. PMIDs: 17661816, 17024664, 27539324, CIViC EIDs (https://civicdb.org): 5748, 5730. Two commercial laboratories report 1 case each, both with a history of VHL-related cancers. One had an additional clinical diagnosis of VHL and a first degree relative with multiple VHL-related cancers in age 30-40yrs who was also VHL positive (PS4_Moderate). Although PP3 was not applied due to use of PVS1, we include the note that multiple splice predictors were used to evaluate the splice site. VarSeak supports the impact of disrupting this canonical splice site (Class 5) and the Splice AI score is 0.93, indicating impact on splicing. In summary, this variant meets the criteria to be classified as Pathogenic for autosomal-dominant von Hippel-Lindau disease (VHL disease) based on the ACMG/AMP criteria applied, as specified by the ClinGen VHL VCEP Version 1.0 (Specifications approval date: 02/26/2024. Variant Approval Date 06/25/2024).
Met criteria codes
PVS1
This is a canonical splice site within the 1st intron, and is predicted to undergo NMD.
PS4_Moderate
This variant has been reported in 1 study, in a case with unilateral pheochromocytoma and screened for SDHB/C/D and RET (0.5 pts) (PMID:27539324) Two commercial laboratories report 1 case each. One has pancreatic and renal cysts and a sibling with VHL disease (1pt) and the other has VHL spectrum tumors noted (0.5pt). According to the VHL VCEP PS4 proband counting for Danish (1pt / proband), Consistent (0.5 pts / proband) and Nonspecific (0.25pts / proband) phenotypes, 2 points achieves (PS4_Moderate).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
Curation History
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