9-100578376-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001018116.2(CAVIN4):c.233C>T(p.Ser78Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00125 in 1,613,944 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001018116.2 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 |
---|---|---|---|---|---|---|---|---|
CAVIN4 | NM_001018116.2 | c.233C>T | p.Ser78Leu | missense_variant | Exon 1 of 2 | ENST00000307584.6 | NP_001018126.1 | |
CAVIN4 | XM_047423346.1 | c.209C>T | p.Ser70Leu | missense_variant | Exon 2 of 3 | XP_047279302.1 | ||
CAVIN4 | XM_047423347.1 | c.21+1421C>T | intron_variant | Intron 1 of 1 | XP_047279303.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00645 AC: 981AN: 152018Hom.: 7 Cov.: 32
GnomAD3 exomes AF: 0.00163 AC: 410AN: 251236Hom.: 2 AF XY: 0.00117 AC XY: 159AN XY: 135752
GnomAD4 exome AF: 0.000703 AC: 1027AN: 1461808Hom.: 10 Cov.: 33 AF XY: 0.000579 AC XY: 421AN XY: 727214
GnomAD4 genome AF: 0.00646 AC: 983AN: 152136Hom.: 7 Cov.: 32 AF XY: 0.00633 AC XY: 471AN XY: 74372
ClinVar
Submissions by phenotype
not specified Benign:2
Ser78Leu in exon 1 of MURC: This variant is not expected to have clinical signif icance because it has been identified in 2.3% (100/4406) of African American chr omosomes from a broad population by the NHLBI Exome Sequencing Project (http://e vs.gs.washington.edu/EVS; dbSNP rs73657328). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at