3-10141843-A-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_000551.4(VHL):c.-5A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000174 in 1,535,018 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000551.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VHL | NM_000551.4 | c.-5A>C | 5_prime_UTR_variant | Exon 1 of 3 | ENST00000256474.3 | NP_000542.1 | ||
VHL | NM_001354723.2 | c.-5A>C | 5_prime_UTR_variant | Exon 1 of 3 | NP_001341652.1 | |||
VHL | NM_198156.3 | c.-5A>C | 5_prime_UTR_variant | Exon 1 of 2 | NP_937799.1 | |||
VHL | NR_176335.1 | n.66A>C | non_coding_transcript_exon_variant | Exon 1 of 4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000946 AC: 144AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000169 AC: 23AN: 135964Hom.: 0 AF XY: 0.000178 AC XY: 13AN XY: 73074
GnomAD4 exome AF: 0.0000882 AC: 122AN: 1382756Hom.: 1 Cov.: 32 AF XY: 0.0000823 AC XY: 56AN XY: 680832
GnomAD4 genome AF: 0.000952 AC: 145AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.000940 AC XY: 70AN XY: 74448
ClinVar
Submissions by phenotype
Von Hippel-Lindau syndrome Benign:2
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This variant is considered likely benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. -
not provided Benign:2
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This variant is associated with the following publications: (PMID: 29790589) -
Hereditary cancer-predisposing syndrome Benign:2
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This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not specified Uncertain:1
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Von Hippel-Lindau syndrome;C1837915:Chuvash polycythemia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at