chr1-26696484-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_006015.6(ARID1A):c.81C>T(p.Ala27Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,249,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_006015.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.81C>T | p.Ala27Ala | synonymous_variant | Exon 1 of 20 | 1 | NM_006015.6 | ENSP00000320485.7 | ||
ARID1A | ENST00000457599.6 | c.81C>T | p.Ala27Ala | synonymous_variant | Exon 1 of 20 | 5 | ENSP00000387636.2 | |||
ARID1A | ENST00000430799.7 | c.-13+2867C>T | intron_variant | Intron 1 of 19 | 5 | ENSP00000390317.3 | ||||
ARID1A | ENST00000637465.1 | c.-13+384C>T | intron_variant | Intron 1 of 2 | 5 | ENSP00000490650.1 |
Frequencies
GnomAD3 genomes AF: 0.0000332 AC: 5AN: 150798Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000364 AC: 40AN: 1098574Hom.: 0 Cov.: 35 AF XY: 0.0000304 AC XY: 16AN XY: 526330
GnomAD4 genome AF: 0.0000332 AC: 5AN: 150798Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73644
ClinVar
Submissions by phenotype
ARID1A-related disorder Benign:1
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