15-63327205-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001218.5(CA12):c.936C>T(p.Gly312Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000273 in 1,613,878 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 (no stars).
Frequency
Consequence
NM_001218.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CA12 | ENST00000178638.8 | c.936C>T | p.Gly312Gly | synonymous_variant | Exon 10 of 11 | 1 | NM_001218.5 | ENSP00000178638.3 | ||
CA12 | ENST00000344366.7 | c.903C>T | p.Gly301Gly | synonymous_variant | Exon 9 of 10 | 1 | ENSP00000343088.3 | |||
CA12 | ENST00000422263.2 | c.723C>T | p.Gly241Gly | synonymous_variant | Exon 8 of 9 | 2 | ENSP00000403028.2 | |||
CA12 | ENST00000560666.1 | n.146C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251296Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135830
GnomAD4 exome AF: 0.000287 AC: 420AN: 1461674Hom.: 0 Cov.: 31 AF XY: 0.000267 AC XY: 194AN XY: 727140
GnomAD4 genome AF: 0.000131 AC: 20AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74356
ClinVar
Submissions by phenotype
CA12-related disorder Benign:1
This variant is classified as likely 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