rs37133
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000722.4(CACNA2D1):c.1279T>C(p.Leu427=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00412 in 1,578,384 control chromosomes in the GnomAD database, including 217 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L427L) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA2D1 | NM_000722.4 | c.1279T>C | p.Leu427= | synonymous_variant | 15/39 | ENST00000356860.8 | |
CACNA2D1-AS1 | NR_110076.1 | n.86+2975A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA2D1 | ENST00000356860.8 | c.1279T>C | p.Leu427= | synonymous_variant | 15/39 | 1 | NM_000722.4 | ||
CACNA2D1-AS1 | ENST00000439234.5 | n.86+2975A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0206 AC: 3053AN: 148268Hom.: 99 Cov.: 32
GnomAD3 exomes AF: 0.00587 AC: 1466AN: 249652Hom.: 61 AF XY: 0.00453 AC XY: 611AN XY: 134900
GnomAD4 exome AF: 0.00241 AC: 3442AN: 1430004Hom.: 118 Cov.: 25 AF XY: 0.00212 AC XY: 1511AN XY: 713242
GnomAD4 genome ? AF: 0.0206 AC: 3060AN: 148380Hom.: 99 Cov.: 32 AF XY: 0.0203 AC XY: 1466AN XY: 72330
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2016 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 03, 2017 | - - |
Brugada syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 16, 2015 | This alteration is classified as 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