chr3-53740333-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS1
The NM_000720.4(CACNA1D):āc.2865G>Cā(p.Leu955=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00047 in 1,607,828 control chromosomes in the GnomAD database, including 1 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. L955L) has been classified as Likely benign.
Frequency
Consequence
NM_000720.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1D | NM_000720.4 | c.2865G>C | p.Leu955= | synonymous_variant | 22/49 | ENST00000288139.11 | |
CACNA1D | NM_001128840.3 | c.2805G>C | p.Leu935= | synonymous_variant | 21/48 | ENST00000350061.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1D | ENST00000288139.11 | c.2865G>C | p.Leu955= | synonymous_variant | 22/49 | 1 | NM_000720.4 | P2 | |
CACNA1D | ENST00000350061.11 | c.2805G>C | p.Leu935= | synonymous_variant | 21/48 | 1 | NM_001128840.3 |
Frequencies
GnomAD3 genomes AF: 0.000992 AC: 151AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000668 AC: 168AN: 251420Hom.: 1 AF XY: 0.000640 AC XY: 87AN XY: 135882
GnomAD4 exome AF: 0.000415 AC: 604AN: 1455520Hom.: 1 Cov.: 27 AF XY: 0.000400 AC XY: 290AN XY: 724710
GnomAD4 genome AF: 0.000991 AC: 151AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000980 AC XY: 73AN XY: 74484
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 28, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 30, 2020 | - - |
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 21, 2017 | p.Leu955Leu in exon 22 of CACNA1D: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 0.23% (55/24024 ) of African chromosomes by the Genome Aggregation Database (gnomAD, http://gnom ad.broadinstitute.org/; dbSNP rs150266932). ACMG/AMP criteria applied: BS1, BP7. - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at