chrX-70277755-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004312.3(ARR3):āc.649A>Gā(p.Ile217Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,208,709 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 118 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 Likely benign (ā ).
Frequency
Consequence
NM_004312.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARR3 | NM_004312.3 | c.649A>G | p.Ile217Val | missense_variant | 10/17 | ENST00000307959.9 | |
ARR3 | XM_047442105.1 | c.673A>G | p.Ile225Val | missense_variant | 9/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARR3 | ENST00000307959.9 | c.649A>G | p.Ile217Val | missense_variant | 10/17 | 1 | NM_004312.3 | P1 | |
ARR3 | ENST00000374495.7 | c.649A>G | p.Ile217Val | missense_variant | 10/16 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000359 AC: 40AN: 111451Hom.: 0 Cov.: 23 AF XY: 0.000297 AC XY: 10AN XY: 33663
GnomAD3 exomes AF: 0.000376 AC: 68AN: 180711Hom.: 0 AF XY: 0.000306 AC XY: 20AN XY: 65383
GnomAD4 exome AF: 0.000283 AC: 310AN: 1097258Hom.: 0 Cov.: 31 AF XY: 0.000298 AC XY: 108AN XY: 362662
GnomAD4 genome AF: 0.000359 AC: 40AN: 111451Hom.: 0 Cov.: 23 AF XY: 0.000297 AC XY: 10AN XY: 33663
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | ARR3: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at