chr7-116506073-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_198212.3(CAV2):c.253C>T(p.Arg85Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 1,613,866 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_198212.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAV2 | NM_001233.5 | c.441C>T | p.Ser147Ser | synonymous_variant | Exon 3 of 3 | ENST00000222693.5 | NP_001224.1 | |
CAV2 | NM_198212.3 | c.253C>T | p.Arg85Cys | missense_variant | Exon 2 of 2 | NP_937855.1 | ||
CAV2 | NM_001206747.2 | c.402C>T | p.Ser134Ser | synonymous_variant | Exon 3 of 3 | NP_001193676.1 | ||
CAV2 | NM_001206748.2 | c.192C>T | p.Ser64Ser | synonymous_variant | Exon 2 of 2 | NP_001193677.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00231 AC: 351AN: 152112Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00475 AC: 1195AN: 251432Hom.: 34 AF XY: 0.00435 AC XY: 591AN XY: 135882
GnomAD4 exome AF: 0.00169 AC: 2476AN: 1461636Hom.: 72 Cov.: 31 AF XY: 0.00166 AC XY: 1204AN XY: 727144
GnomAD4 genome AF: 0.00231 AC: 351AN: 152230Hom.: 7 Cov.: 33 AF XY: 0.00253 AC XY: 188AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at