chr1-26696885-T-TCGC
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PM4_SupportingBP6BS1BS2
The NM_006015.6(ARID1A):c.492_494dup(p.Ala166dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000726 in 1,348,620 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V161V) has been classified as Likely benign.
Frequency
Consequence
NM_006015.6 inframe_insertion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.492_494dup | p.Ala166dup | inframe_insertion | 1/20 | ENST00000324856.13 | |
ARID1A | NM_139135.4 | c.492_494dup | p.Ala166dup | inframe_insertion | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.492_494dup | p.Ala166dup | inframe_insertion | 1/20 | 1 | NM_006015.6 | ||
ARID1A | ENST00000457599.6 | c.492_494dup | p.Ala166dup | inframe_insertion | 1/20 | 5 | |||
ARID1A | ENST00000430799.7 | c.-13+3278_-13+3280dup | intron_variant | 5 | A2 | ||||
ARID1A | ENST00000637465.1 | c.-13+795_-13+797dup | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000425 AC: 62AN: 145868Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000839 AC: 2AN: 23828Hom.: 0 AF XY: 0.0000758 AC XY: 1AN XY: 13200
GnomAD4 exome AF: 0.000763 AC: 917AN: 1202620Hom.: 0 Cov.: 35 AF XY: 0.000689 AC XY: 402AN XY: 583278
GnomAD4 genome AF: 0.000425 AC: 62AN: 146000Hom.: 0 Cov.: 32 AF XY: 0.000323 AC XY: 23AN XY: 71308
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 11, 2019 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 22, 2015 | - - |
ARID1A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 27, 2023 | This variant is classified as likely 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