15-63340370-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001218.5(CA12):c.665G>A(p.Arg222Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00154 in 1,614,118 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R222W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001218.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CA12 | NM_001218.5 | c.665G>A | p.Arg222Gln | missense_variant | 7/11 | ENST00000178638.8 | |
LOC124903506 | XR_007064676.1 | n.768-1444C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CA12 | ENST00000178638.8 | c.665G>A | p.Arg222Gln | missense_variant | 7/11 | 1 | NM_001218.5 | A1 | |
CA12 | ENST00000344366.7 | c.665G>A | p.Arg222Gln | missense_variant | 7/10 | 1 | P4 | ||
CA12 | ENST00000422263.2 | c.485G>A | p.Arg162Gln | missense_variant | 6/9 | 2 | |||
CA12 | ENST00000558287.1 | n.213G>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000881 AC: 134AN: 152126Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00326 AC: 820AN: 251456Hom.: 22 AF XY: 0.00442 AC XY: 600AN XY: 135900
GnomAD4 exome AF: 0.00161 AC: 2355AN: 1461874Hom.: 56 Cov.: 31 AF XY: 0.00226 AC XY: 1644AN XY: 727236
GnomAD4 genome AF: 0.000880 AC: 134AN: 152244Hom.: 4 Cov.: 32 AF XY: 0.00128 AC XY: 95AN XY: 74426
ClinVar
Submissions by phenotype
CA12-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at