9-35675868-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001216.3(CA9):c.541G>A(p.Glu181Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,606,280 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_001216.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA9 | NM_001216.3 | c.541G>A | p.Glu181Lys | missense_variant | 3/11 | ENST00000378357.9 | NP_001207.2 | |
CA9 | XM_047423849.1 | c.541G>A | p.Glu181Lys | missense_variant | 3/6 | XP_047279805.1 | ||
CA9 | XM_047423850.1 | c.541G>A | p.Glu181Lys | missense_variant | 3/6 | XP_047279806.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000440 AC: 67AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000103 AC: 24AN: 233144Hom.: 0 AF XY: 0.0000853 AC XY: 11AN XY: 129020
GnomAD4 exome AF: 0.0000688 AC: 100AN: 1453964Hom.: 0 Cov.: 33 AF XY: 0.0000567 AC XY: 41AN XY: 723564
GnomAD4 genome AF: 0.000446 AC: 68AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 28, 2023 | The c.541G>A (p.E181K) alteration is located in exon 3 (coding exon 3) of the CA9 gene. This alteration results from a G to A substitution at nucleotide position 541, causing the glutamic acid (E) at amino acid position 181 to be replaced by a lysine (K). 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