chr7-151049121-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004769.4(ASIC3):c.236G>A(p.Arg79Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004769.4 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 |
---|---|---|---|---|---|---|---|
ASIC3 | NM_004769.4 | c.236G>A | p.Arg79Gln | missense_variant | 1/11 | ENST00000349064.10 | |
ASIC3 | NM_020321.3 | c.236G>A | p.Arg79Gln | missense_variant | 1/11 | ||
ASIC3 | NM_020322.3 | c.236G>A | p.Arg79Gln | missense_variant | 1/10 | ||
ASIC3 | NR_046401.1 | n.830G>A | non_coding_transcript_exon_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASIC3 | ENST00000349064.10 | c.236G>A | p.Arg79Gln | missense_variant | 1/11 | 1 | NM_004769.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251254Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135878
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461562Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727110
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.236G>A (p.R79Q) alteration is located in exon 1 (coding exon 1) of the ASIC3 gene. This alteration results from a G to A substitution at nucleotide position 236, causing the arginine (R) at amino acid position 79 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