rs118203931
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 4P and 14B. PM1PM5BP4_StrongBP6_ModerateBS1BS2
The NM_000067.3(CA2):āc.52A>Cā(p.Lys18Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000242 in 1,614,032 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K18E) has been classified as Pathogenic.
Frequency
Consequence
NM_000067.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CA2 | NM_000067.3 | c.52A>C | p.Lys18Gln | missense_variant | 2/7 | ENST00000285379.10 | |
CA2 | NM_001293675.2 | c.-133A>C | 5_prime_UTR_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CA2 | ENST00000285379.10 | c.52A>C | p.Lys18Gln | missense_variant | 2/7 | 1 | NM_000067.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152180Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000461 AC: 116AN: 251464Hom.: 3 AF XY: 0.000611 AC XY: 83AN XY: 135910
GnomAD4 exome AF: 0.000254 AC: 371AN: 1461734Hom.: 6 Cov.: 31 AF XY: 0.000363 AC XY: 264AN XY: 727188
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152298Hom.: 1 Cov.: 31 AF XY: 0.000188 AC XY: 14AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at