16-87888240-T-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001739.2(CA5A):c.807A>T(p.Ala269Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 1,613,382 control chromosomes in the GnomAD database, including 31,937 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001739.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA5A | NM_001739.2 | c.807A>T | p.Ala269Ala | synonymous_variant | Exon 7 of 7 | ENST00000649794.3 | NP_001730.1 | |
CA5A | NM_001367225.1 | c.774+3559A>T | intron_variant | Intron 6 of 6 | NP_001354154.1 | |||
CA5A | NR_159798.1 | n.994A>T | non_coding_transcript_exon_variant | Exon 8 of 8 | ||||
CA5A | NR_159799.1 | n.767A>T | non_coding_transcript_exon_variant | Exon 6 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.174 AC: 26391AN: 151892Hom.: 2449 Cov.: 32
GnomAD3 exomes AF: 0.183 AC: 45841AN: 250754Hom.: 4598 AF XY: 0.190 AC XY: 25736AN XY: 135506
GnomAD4 exome AF: 0.198 AC: 288821AN: 1461372Hom.: 29484 Cov.: 32 AF XY: 0.201 AC XY: 145884AN XY: 726964
GnomAD4 genome AF: 0.174 AC: 26404AN: 152010Hom.: 2453 Cov.: 32 AF XY: 0.172 AC XY: 12803AN XY: 74292
ClinVar
Submissions by phenotype
Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency Benign:2
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not provided Benign:2
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at