rs571264557
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_006015.6(ARID1A):c.358C>T(p.Pro120Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000915 in 1,352,836 control chromosomes in the GnomAD database, including 16 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 Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P120L) has been classified as Benign.
Frequency
Consequence
NM_006015.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.358C>T | p.Pro120Ser | missense_variant | 1/20 | ENST00000324856.13 | |
ARID1A | NM_139135.4 | c.358C>T | p.Pro120Ser | missense_variant | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.358C>T | p.Pro120Ser | missense_variant | 1/20 | 1 | NM_006015.6 | ||
ARID1A | ENST00000457599.6 | c.358C>T | p.Pro120Ser | missense_variant | 1/20 | 5 | |||
ARID1A | ENST00000430799.7 | c.-13+3144C>T | intron_variant | 5 | A2 | ||||
ARID1A | ENST00000637465.1 | c.-13+661C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00516 AC: 778AN: 150658Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.000271 AC: 4AN: 14766Hom.: 0 AF XY: 0.000222 AC XY: 2AN XY: 9012
GnomAD4 exome AF: 0.000384 AC: 461AN: 1202068Hom.: 6 Cov.: 35 AF XY: 0.000317 AC XY: 185AN XY: 584438
GnomAD4 genome ? AF: 0.00515 AC: 777AN: 150768Hom.: 10 Cov.: 32 AF XY: 0.00521 AC XY: 384AN XY: 73692
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | ARID1A: PP2, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 23, 2020 | This variant is associated with the following publications: (PMID: 23906836) - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 26, 2016 | - - |
ARID1A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at