chrX-70278572-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004312.3(ARR3):c.836G>A(p.Cys279Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,210,079 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 67 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004312.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARR3 | NM_004312.3 | c.836G>A | p.Cys279Tyr | missense_variant | 12/17 | ENST00000307959.9 | |
ARR3 | XM_047442105.1 | c.860G>A | p.Cys287Tyr | missense_variant | 11/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARR3 | ENST00000307959.9 | c.836G>A | p.Cys279Tyr | missense_variant | 12/17 | 1 | NM_004312.3 | P1 | |
ARR3 | ENST00000374495.7 | c.836G>A | p.Cys279Tyr | missense_variant | 12/16 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000713 AC: 8AN: 112197Hom.: 0 Cov.: 23 AF XY: 0.0000582 AC XY: 2AN XY: 34353
GnomAD3 exomes AF: 0.000142 AC: 26AN: 183077Hom.: 0 AF XY: 0.000163 AC XY: 11AN XY: 67529
GnomAD4 exome AF: 0.000188 AC: 206AN: 1097882Hom.: 0 Cov.: 30 AF XY: 0.000179 AC XY: 65AN XY: 363248
GnomAD4 genome AF: 0.0000713 AC: 8AN: 112197Hom.: 0 Cov.: 23 AF XY: 0.0000582 AC XY: 2AN XY: 34353
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.836G>A (p.C279Y) alteration is located in exon 12 (coding exon 11) of the ARR3 gene. This alteration results from a G to A substitution at nucleotide position 836, causing the cysteine (C) at amino acid position 279 to be replaced by a tyrosine (Y). 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