7-81997206-T-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_000722.4(CACNA2D1):āc.1635A>Cā(p.Ala545=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000996 in 1,607,018 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 Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. A545A) has been classified as Likely benign.
Frequency
Consequence
NM_000722.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA2D1 | NM_000722.4 | c.1635A>C | p.Ala545= | synonymous_variant | 19/39 | ENST00000356860.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA2D1 | ENST00000356860.8 | c.1635A>C | p.Ala545= | synonymous_variant | 19/39 | 1 | NM_000722.4 | ||
CACNA2D1 | ENST00000443883.2 | c.1692A>C | p.Ala564= | synonymous_variant | 20/39 | 5 | P1 | ||
CACNA2D1 | ENST00000705962.1 | c.1536A>C | p.Ala512= | synonymous_variant | 19/38 | ||||
CACNA2D1 | ENST00000705961.1 | c.1404A>C | p.Ala468= | synonymous_variant | 17/37 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251092Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135678
GnomAD4 exome AF: 0.00000894 AC: 13AN: 1454906Hom.: 0 Cov.: 27 AF XY: 0.00000966 AC XY: 7AN XY: 724398
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
Brugada syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 26, 2020 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at