8-85333605-AGT-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001128831.4(CA1):c.368_369delAC(p.His123LeufsTer11) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000412 in 1,457,148 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001128831.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250342Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135316
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1457148Hom.: 0 AF XY: 0.00000552 AC XY: 4AN XY: 725168
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Renal tubular acidosis;C0035579:Rickets;C0220981:Metabolic acidosis Uncertain:1
A role of this CA1 gene in renal tubular acidosis was suggested earlier, however no disorder has been associated with this gene till date (Shapira et al. J Clin Invest 1974). Another gene of this family (CA2) is known to cause autosomal recessive osteopetrosis with renal tubular acidosis (MIM#259730). The c.368_369del variant is present in publicly available databases like Exome Aggregation Consortium (ExAC), Genome Aggregation Database (gnomAD) and dbSNP only in heterozygous state (minor allele frequency < 0.00001). The variant is not present in our in-house exome database. The variant was not reported to OMIM, ClinVar and Human Genome Mutation Database (HGMD) in any other affected individuals. In-silico pathogenicity prediction programs like MutationTaster2, CADD etc. predicted this variant as likely deleterious. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at