3-119383206-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_020754.4(ARHGAP31):c.662C>T(p.Pro221Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00183 in 1,614,086 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_020754.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGAP31 | NM_020754.4 | c.662C>T | p.Pro221Leu | missense_variant | 6/12 | ENST00000264245.9 | NP_065805.2 | |
ARHGAP31 | XM_006713714.4 | c.662C>T | p.Pro221Leu | missense_variant | 6/12 | XP_006713777.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGAP31 | ENST00000264245.9 | c.662C>T | p.Pro221Leu | missense_variant | 6/12 | 1 | NM_020754.4 | ENSP00000264245 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00134 AC: 204AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00164 AC: 409AN: 249574Hom.: 1 AF XY: 0.00148 AC XY: 201AN XY: 135404
GnomAD4 exome AF: 0.00189 AC: 2756AN: 1461860Hom.: 9 Cov.: 32 AF XY: 0.00182 AC XY: 1326AN XY: 727232
GnomAD4 genome AF: 0.00134 AC: 204AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.00116 AC XY: 86AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 02, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | ARHGAP31: BS1, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 12, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at