7-116500276-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001233.5(CAV2):c.167T>A(p.Val56Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,614,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001233.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAV2 | NM_001233.5 | c.167T>A | p.Val56Glu | missense_variant | Exon 2 of 3 | ENST00000222693.5 | NP_001224.1 | |
CAV2 | NM_001206747.2 | c.128T>A | p.Val43Glu | missense_variant | Exon 2 of 3 | NP_001193676.1 | ||
CAV2 | NM_001206748.2 | c.-83T>A | 5_prime_UTR_variant | Exon 1 of 2 | NP_001193677.1 | |||
CAV2 | NM_198212.3 | c.150+345T>A | intron_variant | Intron 1 of 1 | NP_937855.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250962Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135618
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461682Hom.: 0 Cov.: 38 AF XY: 0.00000550 AC XY: 4AN XY: 727138
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.167T>A (p.V56E) alteration is located in exon 2 (coding exon 2) of the CAV2 gene. This alteration results from a T to A substitution at nucleotide position 167, causing the valine (V) at amino acid position 56 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at