16-87888259-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001739.2(CA5A):c.788G>A(p.Arg263His) variant causes a missense change. The variant allele was found at a frequency of 0.000613 in 1,613,076 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R263C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001739.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA5A | NM_001739.2 | c.788G>A | p.Arg263His | missense_variant | Exon 7 of 7 | ENST00000649794.3 | NP_001730.1 | |
CA5A | NM_001367225.1 | c.774+3540G>A | intron_variant | Intron 6 of 6 | NP_001354154.1 | |||
CA5A | NR_159798.1 | n.975G>A | non_coding_transcript_exon_variant | Exon 8 of 8 | ||||
CA5A | NR_159799.1 | n.748G>A | non_coding_transcript_exon_variant | Exon 6 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152026Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00131 AC: 328AN: 250168Hom.: 5 AF XY: 0.00180 AC XY: 244AN XY: 135232
GnomAD4 exome AF: 0.000637 AC: 930AN: 1460934Hom.: 15 Cov.: 31 AF XY: 0.000930 AC XY: 676AN XY: 726694
GnomAD4 genome AF: 0.000388 AC: 59AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.000578 AC XY: 43AN XY: 74392
ClinVar
Submissions by phenotype
Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency Uncertain:1Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at