rs369673473
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The ENST00000399655.6(CACNA1C):c.537C>T(p.Ile179=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000837 in 1,601,044 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 (★★). Synonymous variant affecting the same amino acid position (i.e. I179I) has been classified as Likely benign.
Frequency
Consequence
ENST00000399655.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.537C>T | p.Ile179= | synonymous_variant | 4/47 | ENST00000399655.6 | NP_000710.5 | |
CACNA1C | NM_001167623.2 | c.537C>T | p.Ile179= | synonymous_variant | 4/47 | ENST00000399603.6 | NP_001161095.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.537C>T | p.Ile179= | synonymous_variant | 4/47 | 5 | NM_001167623.2 | ENSP00000382512 | ||
CACNA1C | ENST00000399655.6 | c.537C>T | p.Ile179= | synonymous_variant | 4/47 | 1 | NM_000719.7 | ENSP00000382563 | ||
ENST00000649808.1 | n.208+118G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000434 AC: 66AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000115 AC: 27AN: 235418Hom.: 0 AF XY: 0.000102 AC XY: 13AN XY: 127240
GnomAD4 exome AF: 0.0000469 AC: 68AN: 1448892Hom.: 0 Cov.: 28 AF XY: 0.0000389 AC XY: 28AN XY: 720222
GnomAD4 genome AF: 0.000434 AC: 66AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.000417 AC XY: 31AN XY: 74316
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2016 | 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