rs199538058
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_000719.7(CACNA1C):c.5214C>A(p.Gly1738Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,613,558 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G1738G) has been classified as Benign.
Frequency
Consequence
NM_000719.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | ENST00000399655.6 | NP_000710.5 | |
CACNA1C | NM_001167623.2 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | ENST00000399603.6 | NP_001161095.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | 5 | NM_001167623.2 | ENSP00000382512.1 | ||
CACNA1C | ENST00000399655.6 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | 1 | NM_000719.7 | ENSP00000382563.1 | ||
CACNA1C | ENST00000682544.1 | c.5448C>A | p.Gly1816Gly | synonymous_variant | Exon 44 of 50 | ENSP00000507184.1 | ||||
CACNA1C | ENST00000406454.8 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 48 | 5 | ENSP00000385896.3 | |||
CACNA1C | ENST00000399634.6 | c.5181C>A | p.Gly1727Gly | synonymous_variant | Exon 41 of 47 | 5 | ENSP00000382542.2 | |||
CACNA1C | ENST00000683824.1 | c.5379C>A | p.Gly1793Gly | synonymous_variant | Exon 43 of 48 | ENSP00000507867.1 | ||||
CACNA1C | ENST00000347598.9 | c.5358C>A | p.Gly1786Gly | synonymous_variant | Exon 44 of 49 | 1 | ENSP00000266376.6 | |||
CACNA1C | ENST00000344100.7 | c.5337C>A | p.Gly1779Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000341092.3 | |||
CACNA1C | ENST00000327702.12 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 48 | 1 | ENSP00000329877.7 | |||
CACNA1C | ENST00000399617.6 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 48 | 5 | ENSP00000382526.1 | |||
CACNA1C | ENST00000682462.1 | c.5304C>A | p.Gly1768Gly | synonymous_variant | Exon 42 of 47 | ENSP00000507105.1 | ||||
CACNA1C | ENST00000683781.1 | c.5304C>A | p.Gly1768Gly | synonymous_variant | Exon 42 of 47 | ENSP00000507434.1 | ||||
CACNA1C | ENST00000683840.1 | c.5304C>A | p.Gly1768Gly | synonymous_variant | Exon 42 of 47 | ENSP00000507612.1 | ||||
CACNA1C | ENST00000683956.1 | c.5304C>A | p.Gly1768Gly | synonymous_variant | Exon 42 of 47 | ENSP00000506882.1 | ||||
CACNA1C | ENST00000399638.5 | c.5298C>A | p.Gly1766Gly | synonymous_variant | Exon 43 of 48 | 1 | ENSP00000382547.1 | |||
CACNA1C | ENST00000335762.10 | c.5289C>A | p.Gly1763Gly | synonymous_variant | Exon 43 of 48 | 5 | ENSP00000336982.5 | |||
CACNA1C | ENST00000399606.5 | c.5274C>A | p.Gly1758Gly | synonymous_variant | Exon 43 of 48 | 1 | ENSP00000382515.1 | |||
CACNA1C | ENST00000399621.5 | c.5271C>A | p.Gly1757Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382530.1 | |||
CACNA1C | ENST00000399637.5 | c.5271C>A | p.Gly1757Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382546.1 | |||
CACNA1C | ENST00000402845.7 | c.5271C>A | p.Gly1757Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000385724.3 | |||
CACNA1C | ENST00000399629.5 | c.5265C>A | p.Gly1755Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382537.1 | |||
CACNA1C | ENST00000682336.1 | c.5256C>A | p.Gly1752Gly | synonymous_variant | Exon 42 of 47 | ENSP00000507898.1 | ||||
CACNA1C | ENST00000399591.5 | c.5238C>A | p.Gly1746Gly | synonymous_variant | Exon 41 of 46 | 1 | ENSP00000382500.1 | |||
CACNA1C | ENST00000399595.5 | c.5238C>A | p.Gly1746Gly | synonymous_variant | Exon 41 of 46 | 1 | ENSP00000382504.1 | |||
CACNA1C | ENST00000399649.5 | c.5232C>A | p.Gly1744Gly | synonymous_variant | Exon 41 of 46 | 1 | ENSP00000382557.1 | |||
CACNA1C | ENST00000399597.5 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382506.1 | |||
CACNA1C | ENST00000399601.5 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382510.1 | |||
CACNA1C | ENST00000399641.6 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382549.1 | |||
CACNA1C | ENST00000399644.5 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | 1 | ENSP00000382552.1 | |||
CACNA1C | ENST00000682835.1 | c.5214C>A | p.Gly1738Gly | synonymous_variant | Exon 42 of 47 | ENSP00000507282.1 | ||||
CACNA1C | ENST00000683482.1 | c.5205C>A | p.Gly1735Gly | synonymous_variant | Exon 42 of 47 | ENSP00000507169.1 | ||||
CACNA1C | ENST00000682686.1 | c.5181C>A | p.Gly1727Gly | synonymous_variant | Exon 41 of 46 | ENSP00000507309.1 |
Frequencies
GnomAD3 genomes AF: 0.00114 AC: 173AN: 152232Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00127 AC: 313AN: 247232Hom.: 0 AF XY: 0.00132 AC XY: 178AN XY: 134350
GnomAD4 exome AF: 0.00134 AC: 1965AN: 1461208Hom.: 3 Cov.: 31 AF XY: 0.00139 AC XY: 1009AN XY: 726874
GnomAD4 genome AF: 0.00114 AC: 173AN: 152350Hom.: 1 Cov.: 33 AF XY: 0.00105 AC XY: 78AN XY: 74496
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
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CACNA1C: BP4, BP7 -
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not specified Benign:3
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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. -
Long QT syndrome Benign:1
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Cardiovascular phenotype Benign:1
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