19-16479197-C-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_145046.5(CALR3):c.1089G>T(p.Leu363=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,014 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. L363L) has been classified as Benign.
Frequency
Consequence
NM_145046.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALR3 | NM_145046.5 | c.1089G>T | p.Leu363= | synonymous_variant | 9/9 | ENST00000269881.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALR3 | ENST00000269881.8 | c.1089G>T | p.Leu363= | synonymous_variant | 9/9 | 1 | NM_145046.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152124Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727248
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74302
ClinVar
Submissions by phenotype
Hypertrophic cardiomyopathy 19 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 06, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at