chr12-53715942-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020898.3(CALCOCO1):c.1111G>A(p.Ala371Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,614,116 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_020898.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALCOCO1 | NM_020898.3 | c.1111G>A | p.Ala371Thr | missense_variant | 9/15 | ENST00000550804.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALCOCO1 | ENST00000550804.6 | c.1111G>A | p.Ala371Thr | missense_variant | 9/15 | 1 | NM_020898.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000841 AC: 128AN: 152126Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251342Hom.: 1 AF XY: 0.000147 AC XY: 20AN XY: 135862
GnomAD4 exome AF: 0.0000711 AC: 104AN: 1461872Hom.: 1 Cov.: 33 AF XY: 0.0000619 AC XY: 45AN XY: 727236
GnomAD4 genome ? AF: 0.000841 AC: 128AN: 152244Hom.: 2 Cov.: 32 AF XY: 0.000860 AC XY: 64AN XY: 74432
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 03, 2022 | 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