rs546507069
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001743.6(CALM2):c.348G>A(p.Lys116Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,412 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 (★★).
Frequency
Consequence
NM_001743.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CALM2 | NM_001743.6 | c.348G>A | p.Lys116Lys | synonymous_variant | Exon 5 of 6 | ENST00000272298.12 | NP_001734.1 | |
CALM2 | NM_001305624.1 | c.492G>A | p.Lys164Lys | synonymous_variant | Exon 6 of 7 | NP_001292553.1 | ||
CALM2 | NM_001305625.2 | c.240G>A | p.Lys80Lys | synonymous_variant | Exon 5 of 6 | NP_001292554.1 | ||
CALM2 | NM_001305626.1 | c.240G>A | p.Lys80Lys | synonymous_variant | Exon 4 of 5 | NP_001292555.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CALM2 | ENST00000272298.12 | c.348G>A | p.Lys116Lys | synonymous_variant | Exon 5 of 6 | 1 | NM_001743.6 | ENSP00000272298.7 | ||
ENSG00000273269 | ENST00000422269.1 | n.101-8780G>A | intron_variant | Intron 2 of 8 | 2 | ENSP00000476793.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250952Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135678
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461108Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 726926
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152304Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74468
ClinVar
Submissions by phenotype
Long QT syndrome 1 Benign:1
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not specified Benign:1
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. -
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