chr3-10141775-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000551.4(VHL):c.-73C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00024 in 1,497,386 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 upstream_gene
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VHL | NM_000551.4 | c.-73C>T | upstream_gene_variant | ENST00000256474.3 | NP_000542.1 | |||
VHL | NM_001354723.2 | c.-73C>T | upstream_gene_variant | NP_001341652.1 | ||||
VHL | NM_198156.3 | c.-73C>T | upstream_gene_variant | NP_937799.1 | ||||
VHL | NR_176335.1 | n.-3C>T | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VHL | ENST00000256474.3 | c.-73C>T | upstream_gene_variant | 1 | NM_000551.4 | ENSP00000256474.3 | ||||
VHL | ENST00000345392.2 | c.-73C>T | upstream_gene_variant | 1 | ENSP00000344757.2 | |||||
VHL | ENST00000696153.1 | c.-73C>T | upstream_gene_variant | ENSP00000512444.1 | ||||||
VHL | ENST00000696142.1 | n.-73C>T | upstream_gene_variant | ENSP00000512434.1 |
Frequencies
GnomAD3 genomes AF: 0.000315 AC: 48AN: 152224Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.000231 AC: 311AN: 1345162Hom.: 0 Cov.: 27 AF XY: 0.000242 AC XY: 161AN XY: 664752
GnomAD4 genome AF: 0.000315 AC: 48AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
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Von Hippel-Lindau syndrome Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Von Hippel-Lindau syndrome;C0031511:Pheochromocytoma;C1837915:Chuvash polycythemia;CN074294:Nonpapillary renal cell carcinoma Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at