rs1455874684
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_000719.7(CACNA1C):c.3988C>T(p.Leu1330=) variant causes a synonymous change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,864 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. L1330L) has been classified as Likely benign.
Frequency
Consequence
NM_000719.7 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.3988C>T | p.Leu1330= | synonymous_variant | 32/47 | ENST00000399655.6 | |
CACNA1C | NM_001167623.2 | c.3988C>T | p.Leu1330= | synonymous_variant | 32/47 | ENST00000399603.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.3988C>T | p.Leu1330= | synonymous_variant | 32/47 | 5 | NM_001167623.2 | ||
CACNA1C | ENST00000399655.6 | c.3988C>T | p.Leu1330= | synonymous_variant | 32/47 | 1 | NM_000719.7 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152174Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249542Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135278
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461690Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 727130
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152174Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 10AN XY: 74342
ClinVar
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | 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