1-26697129-CGCG-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM4_SupportingBS2
The NM_006015.6(ARID1A):c.735_737delGGC(p.Ala246del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00008 in 1,437,200 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006015.6 disruptive_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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.735_737delGGC | p.Ala246del | disruptive_inframe_deletion | Exon 1 of 20 | ENST00000324856.13 | NP_006006.3 | |
ARID1A | NM_139135.4 | c.735_737delGGC | p.Ala246del | disruptive_inframe_deletion | Exon 1 of 20 | NP_624361.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARID1A | ENST00000324856.13 | c.735_737delGGC | p.Ala246del | disruptive_inframe_deletion | Exon 1 of 20 | 1 | NM_006015.6 | ENSP00000320485.7 | ||
ARID1A | ENST00000457599.6 | c.735_737delGGC | p.Ala246del | disruptive_inframe_deletion | Exon 1 of 20 | 5 | ENSP00000387636.2 | |||
ARID1A | ENST00000430799.7 | c.-13+3521_-13+3523delGGC | intron_variant | Intron 1 of 19 | 5 | ENSP00000390317.3 | ||||
ARID1A | ENST00000637465.1 | c.-13+1038_-13+1040delGGC | intron_variant | Intron 1 of 2 | 5 | ENSP00000490650.1 |
Frequencies
GnomAD3 genomes AF: 0.0000331 AC: 5AN: 151218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000719 AC: 4AN: 55646Hom.: 0 AF XY: 0.0000935 AC XY: 3AN XY: 32094
GnomAD4 exome AF: 0.0000855 AC: 110AN: 1285982Hom.: 0 AF XY: 0.0000809 AC XY: 51AN XY: 630762
GnomAD4 genome AF: 0.0000331 AC: 5AN: 151218Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73860
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.735_737del, results in the deletion of 1 amino acid(s) of the ARID1A protein (p.Ala247del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with ARID1A-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at