chr7-45038379-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_031443.4(CCM2):c.157G>A(p.Val53Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0791 in 1,614,010 control chromosomes in the GnomAD database, including 5,764 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. V53V) has been classified as Likely benign.
Frequency
Consequence
NM_031443.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCM2 | NM_031443.4 | c.157G>A | p.Val53Ile | missense_variant | 2/10 | ENST00000258781.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCM2 | ENST00000258781.11 | c.157G>A | p.Val53Ile | missense_variant | 2/10 | 1 | NM_031443.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0604 AC: 9192AN: 152116Hom.: 386 Cov.: 32
GnomAD3 exomes AF: 0.0631 AC: 15863AN: 251384Hom.: 661 AF XY: 0.0635 AC XY: 8628AN XY: 135870
GnomAD4 exome AF: 0.0811 AC: 118554AN: 1461776Hom.: 5378 Cov.: 33 AF XY: 0.0804 AC XY: 58488AN XY: 727192
GnomAD4 genome AF: 0.0604 AC: 9189AN: 152234Hom.: 386 Cov.: 32 AF XY: 0.0569 AC XY: 4236AN XY: 74440
ClinVar
Submissions by phenotype
Cerebral cavernous malformation 2 Benign:4
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Jul 12, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 09, 2018 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at