rs367889013
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006015.6(ARID1A):āc.2123A>Cā(p.Gln708Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,614,050 control chromosomes in the GnomAD database, including 44 homozygotes. 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 ā ).
Frequency
Consequence
NM_006015.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.2123A>C | p.Gln708Pro | missense_variant | 5/20 | ENST00000324856.13 | |
ARID1A | NM_139135.4 | c.2123A>C | p.Gln708Pro | missense_variant | 5/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.2123A>C | p.Gln708Pro | missense_variant | 5/20 | 1 | NM_006015.6 |
Frequencies
GnomAD3 genomes ? AF: 0.000848 AC: 129AN: 152058Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00315 AC: 791AN: 251320Hom.: 18 AF XY: 0.00424 AC XY: 576AN XY: 135858
GnomAD4 exome AF: 0.00152 AC: 2222AN: 1461874Hom.: 43 Cov.: 31 AF XY: 0.00222 AC XY: 1611AN XY: 727240
GnomAD4 genome ? AF: 0.000841 AC: 128AN: 152176Hom.: 1 Cov.: 32 AF XY: 0.00132 AC XY: 98AN XY: 74390
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 08, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | ARID1A: BS1, BS2 - |
not specified Benign:1Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 14, 2016 | - - |
Intellectual disability, autosomal dominant 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at