chr1-26696885-TCGC-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM4_SupportingBS2
The NM_006015.6(ARID1A):c.492_494del(p.Ala167del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000258 in 1,202,438 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. V161V) has been classified as Likely benign.
Frequency
Consequence
NM_006015.6 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.492_494del | p.Ala167del | inframe_deletion | 1/20 | ENST00000324856.13 | |
ARID1A | NM_139135.4 | c.492_494del | p.Ala167del | inframe_deletion | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.492_494del | p.Ala167del | inframe_deletion | 1/20 | 1 | NM_006015.6 | ||
ARID1A | ENST00000457599.6 | c.492_494del | p.Ala167del | inframe_deletion | 1/20 | 5 | |||
ARID1A | ENST00000430799.7 | c.-13+3278_-13+3280del | intron_variant | 5 | A2 | ||||
ARID1A | ENST00000637465.1 | c.-13+795_-13+797del | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.000210 AC: 5AN: 23828Hom.: 0 AF XY: 0.000227 AC XY: 3AN XY: 13200
GnomAD4 exome AF: 0.0000258 AC: 31AN: 1202438Hom.: 0 AF XY: 0.0000394 AC XY: 23AN XY: 583166
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at