chr3-53495165-G-GGAT
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS1_Supporting
The NM_001128840.3(CACNA1D):c.20_22dupTGA(p.Met7dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,606,888 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001128840.3 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.20_22dupTGA | p.Met7dup | disruptive_inframe_insertion | Exon 1 of 49 | ENST00000288139.11 | NP_000711.1 | |
CACNA1D | NM_001128840.3 | c.20_22dupTGA | p.Met7dup | disruptive_inframe_insertion | Exon 1 of 48 | ENST00000350061.11 | NP_001122312.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1D | ENST00000288139.11 | c.20_22dupTGA | p.Met7dup | disruptive_inframe_insertion | Exon 1 of 49 | 1 | NM_000720.4 | ENSP00000288139.3 | ||
CACNA1D | ENST00000350061.11 | c.20_22dupTGA | p.Met7dup | disruptive_inframe_insertion | Exon 1 of 48 | 1 | NM_001128840.3 | ENSP00000288133.5 |
Frequencies
GnomAD3 genomes AF: 0.000231 AC: 35AN: 151204Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000162 AC: 40AN: 247184Hom.: 0 AF XY: 0.000186 AC XY: 25AN XY: 134164
GnomAD4 exome AF: 0.000204 AC: 297AN: 1455684Hom.: 0 Cov.: 33 AF XY: 0.000224 AC XY: 162AN XY: 724360
GnomAD4 genome AF: 0.000231 AC: 35AN: 151204Hom.: 0 Cov.: 31 AF XY: 0.000285 AC XY: 21AN XY: 73798
ClinVar
Submissions by phenotype
not provided Uncertain:2
In-frame duplication in a repetitive region with no known function; Has not been previously published as pathogenic or benign to our knowledge -
BP3 -
Inborn genetic diseases Uncertain:1
Unlikely to be causative of primary aldosteronism, seizures, and neurologic abnormalities (AD) Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at