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.610G>T (p.Glu204Ter)

CA041909

526673 (ClinVar)

Gene: VHL
Condition: von Hippel-Lindau disease
Inheritance Mode: Autosomal dominant inheritance
UUID: dae201a3-af5a-4275-9e46-16b1bbc2104e
Approved on: 2024-06-25
Published on: 2024-06-25

HGVS expressions

NM_000551.4:c.610G>T
NM_000551.4(VHL):c.610G>T (p.Glu204Ter)
NC_000003.12:g.10149933G>T
CM000665.2:g.10149933G>T
NC_000003.11:g.10191617G>T
CM000665.1:g.10191617G>T
NC_000003.10:g.10166617G>T
NG_008212.3:g.13299G>T
ENST00000696142.1:c.*287G>T
ENST00000696143.1:c.746G>T
ENST00000696153.1:c.721G>T
ENST00000256474.3:c.610G>T
ENST00000256474.2:c.610G>T
ENST00000345392.2:c.487G>T
ENST00000477538.1:n.746G>T
NM_000551.3:c.610G>T
NM_198156.2:c.487G>T
NM_001354723.1:c.*164G>T
NM_001354723.2:c.*164G>T
NM_198156.3:c.487G>T
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Uncertain Significance

Met criteria codes 2
PM2_Supporting PVS1_Moderate
Not Met criteria codes 3
BA1 BS2 PS4

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_000551.4(VHL):c.610G>T (p.Glu204Ter) is a truncating variant predicted to cause a premature stop codon in biologically-relevant-exon (the third exon). This is not predicted to lead to nonsense mediated decay, although in VHL a loss-of-function is an established disease mechanism. As the role of the region between amino acids (AA205 -213) is overall unknown, this receives PVS1_Moderate per the VHL VCEP PVS1 decision tree (PVS1_Moderate). The GroupMax Filtering Allele Frequency (95% CI) in gnomAD v4.1.0 is 0.00000028 (2/1112000 from European, Non-Finnish Population). PM2_Supporting can be applied for variants with <= 0.0000015 (0.00015%) frequency in gnomAD (PM2_Supporting). A total of 4 cases between three commercial laboratories did not identify any cases with VHL spectrum tumors, and one case is >= 60yo without VHL spectrum tumors. PS4 is not met, and BS2 is not met. There are no additional reports identified in the literature. In summary, this variant meets the criteria to be classified as Uncertain for autosomal-dominant von Hippel Lindau syndrome (VHL syndrome) 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
PM2_Supporting
The GroupMax Filtering Allele Frequency (95% CI) in gnomAD v4.1.0 is 0.00000028 (2/1112000 from European, Non-Finnish Population). PM2_Supporting can be applied for variants with <= 0.0000015 (0.00015%) frequency in gnomAD (PM2_Supporting).
PVS1_Moderate
A non-NMD truncating variant that disrupts AA205_213 (role of the region in protein is unknown) per PVS1 decision tree.
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
A total of 4 cases between three commercial laboratories does not identify any cases with VHL spectrum tumors, and one case is >= 60yo without VHL spectrum tumors. PS4 is not met, and BS2 is not met.
PS4
A total of 4 cases between three commercial laboratories does not identify any cases with VHL spectrum tumors, and one case is >= 60yo without VHL spectrum tumors. PS4 is not met, and BS2 is not met.
Curation History
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