rs2080253926
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006015.6(ARID1A):c.55C>A(p.Pro19Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000878 in 1,139,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P19A) has been classified as Uncertain significance.
Frequency
Consequence
NM_006015.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.55C>A | p.Pro19Thr | missense_variant | Exon 1 of 20 | ENST00000324856.13 | NP_006006.3 | |
ARID1A | NM_139135.4 | c.55C>A | p.Pro19Thr | missense_variant | Exon 1 of 20 | NP_624361.1 | ||
LOC124900417 | XM_047439473.1 | c.-53G>T | upstream_gene_variant | XP_047295429.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.55C>A | p.Pro19Thr | missense_variant | Exon 1 of 20 | 1 | NM_006015.6 | ENSP00000320485.7 | ||
ARID1A | ENST00000457599.6 | c.55C>A | p.Pro19Thr | missense_variant | Exon 1 of 20 | 5 | ENSP00000387636.2 | |||
ARID1A | ENST00000430799.7 | c.-13+2841C>A | intron_variant | Intron 1 of 19 | 5 | ENSP00000390317.3 | ||||
ARID1A | ENST00000637465.1 | c.-13+358C>A | intron_variant | Intron 1 of 2 | 5 | ENSP00000490650.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 8.78e-7 AC: 1AN: 1139572Hom.: 0 Cov.: 35 AF XY: 0.00000181 AC XY: 1AN XY: 552996
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.