15-63340334-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001218.5(CA12):āc.701T>Cā(p.Val234Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,614,072 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001218.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CA12 | ENST00000178638.8 | c.701T>C | p.Val234Ala | missense_variant | Exon 7 of 11 | 1 | NM_001218.5 | ENSP00000178638.3 | ||
CA12 | ENST00000344366.7 | c.701T>C | p.Val234Ala | missense_variant | Exon 7 of 10 | 1 | ENSP00000343088.3 | |||
CA12 | ENST00000422263.2 | c.521T>C | p.Val174Ala | missense_variant | Exon 6 of 9 | 2 | ENSP00000403028.2 | |||
CA12 | ENST00000558287.1 | n.249T>C | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251474Hom.: 1 AF XY: 0.000118 AC XY: 16AN XY: 135906
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461894Hom.: 2 Cov.: 31 AF XY: 0.0000976 AC XY: 71AN XY: 727248
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.701T>C (p.V234A) alteration is located in exon 7 (coding exon 7) of the CA12 gene. This alteration results from a T to C substitution at nucleotide position 701, causing the valine (V) at amino acid position 234 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at