chr9-35674143-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.184G>A(p.Glu62Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000427 in 1,614,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E62Q) has been classified 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 | UniProt |
---|---|---|---|---|---|---|---|
CA9 | NM_001216.3 | c.184G>A | p.Glu62Lys | missense_variant | 1/11 | ENST00000378357.9 | |
CA9 | XM_047423849.1 | c.184G>A | p.Glu62Lys | missense_variant | 1/6 | ||
CA9 | XM_047423850.1 | c.184G>A | p.Glu62Lys | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CA9 | ENST00000378357.9 | c.184G>A | p.Glu62Lys | missense_variant | 1/11 | 1 | NM_001216.3 | P1 | |
ARHGEF39 | ENST00000490638.5 | c.-428C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/12 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152216Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251260Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135812
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461824Hom.: 0 Cov.: 33 AF XY: 0.0000289 AC XY: 21AN XY: 727206
GnomAD4 genome AF: 0.000197 AC: 30AN: 152334Hom.: 0 Cov.: 31 AF XY: 0.000228 AC XY: 17AN XY: 74488
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at