1-26697129-CGCG-CGCGGCG
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM4_SupportingBP6BS2
The NM_006015.6(ARID1A):c.735_737dupGGC(p.Ala246dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000468 in 1,437,258 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006015.6 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID1A | NM_006015.6 | c.735_737dupGGC | p.Ala246dup | disruptive_inframe_insertion | Exon 1 of 20 | ENST00000324856.13 | NP_006006.3 | |
ARID1A | NM_139135.4 | c.735_737dupGGC | p.Ala246dup | disruptive_inframe_insertion | 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_737dupGGC | p.Ala246dup | disruptive_inframe_insertion | Exon 1 of 20 | 1 | NM_006015.6 | ENSP00000320485.7 | ||
ARID1A | ENST00000457599.6 | c.735_737dupGGC | p.Ala246dup | disruptive_inframe_insertion | Exon 1 of 20 | 5 | ENSP00000387636.2 | |||
ARID1A | ENST00000430799.7 | c.-13+3521_-13+3523dupGGC | intron_variant | Intron 1 of 19 | 5 | ENSP00000390317.3 | ||||
ARID1A | ENST00000637465.1 | c.-13+1038_-13+1040dupGGC | intron_variant | Intron 1 of 2 | 5 | ENSP00000490650.1 |
Frequencies
GnomAD3 genomes AF: 0.000317 AC: 48AN: 151218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000216 AC: 12AN: 55646Hom.: 0 AF XY: 0.000312 AC XY: 10AN XY: 32094
GnomAD4 exome AF: 0.000486 AC: 625AN: 1286040Hom.: 1 Cov.: 35 AF XY: 0.000449 AC XY: 283AN XY: 630792
GnomAD4 genome AF: 0.000317 AC: 48AN: 151218Hom.: 0 Cov.: 32 AF XY: 0.000298 AC XY: 22AN XY: 73860
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
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ARID1A: BP3, BS1 -
not specified Uncertain:1
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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