X-70277497-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_004312.3(ARR3):c.577C>T(p.Pro193Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000189 in 1,209,790 control chromosomes in the GnomAD database, including 1 homozygotes. There are 80 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004312.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARR3 | NM_004312.3 | c.577C>T | p.Pro193Ser | missense_variant | 9/17 | ENST00000307959.9 | |
ARR3 | XM_047442105.1 | c.601C>T | p.Pro201Ser | missense_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARR3 | ENST00000307959.9 | c.577C>T | p.Pro193Ser | missense_variant | 9/17 | 1 | NM_004312.3 | P1 | |
ARR3 | ENST00000374495.7 | c.577C>T | p.Pro193Ser | missense_variant | 9/16 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000312 AC: 35AN: 112172Hom.: 0 Cov.: 23 AF XY: 0.000379 AC XY: 13AN XY: 34322
GnomAD3 exomes AF: 0.000266 AC: 48AN: 180630Hom.: 1 AF XY: 0.000322 AC XY: 21AN XY: 65256
GnomAD4 exome AF: 0.000177 AC: 194AN: 1097618Hom.: 1 Cov.: 32 AF XY: 0.000185 AC XY: 67AN XY: 362992
GnomAD4 genome AF: 0.000312 AC: 35AN: 112172Hom.: 0 Cov.: 23 AF XY: 0.000379 AC XY: 13AN XY: 34322
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | ARR3: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at