chr9-35674143-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001216.3(CA9):āc.184G>Cā(p.Glu62Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,040 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E62K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001216.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CA9 | NM_001216.3 | c.184G>C | p.Glu62Gln | missense_variant | 1/11 | ENST00000378357.9 | |
CA9 | XM_047423849.1 | c.184G>C | p.Glu62Gln | missense_variant | 1/6 | ||
CA9 | XM_047423850.1 | c.184G>C | p.Glu62Gln | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CA9 | ENST00000378357.9 | c.184G>C | p.Glu62Gln | missense_variant | 1/11 | 1 | NM_001216.3 | P1 | |
ARHGEF39 | ENST00000490638.5 | c.-428C>G | 5_prime_UTR_variant, NMD_transcript_variant | 1/12 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461824Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727206
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.184G>C (p.E62Q) alteration is located in exon 1 (coding exon 1) of the CA9 gene. This alteration results from a G to C substitution at nucleotide position 184, causing the glutamic acid (E) at amino acid position 62 to be replaced by a glutamine (Q). 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