GeneBe

rs587779747

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_001374828.1(ARID1B):​c.1173_1193delCGGCGGCGGCGGCGGCGGCGG​(p.Gly392_Gly398del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000000796 in 1,255,596 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 29)
Exomes 𝑓: 8.0e-7 ( 0 hom. )

Consequence

ARID1B
NM_001374828.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.68

Publications

0 publications found
Variant links:
Genes affected
ARID1B (HGNC:18040): (AT-rich interaction domain 1B) This locus encodes an AT-rich DNA interacting domain-containing protein. The encoded protein is a component of the SWI/SNF chromatin remodeling complex and may play a role in cell-cycle activation. The protein encoded by this locus is similar to AT-rich interactive domain-containing protein 1A. These two proteins function as alternative, mutually exclusive ARID-subunits of the SWI/SNF complex. The associated complexes play opposing roles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]
ARID1B Gene-Disease associations (from GenCC):
  • Coffin-Siris syndrome
    Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina, ClinGen
  • Coffin-Siris syndrome 1
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001374828.1

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARID1BNM_001374828.1 linkc.1173_1193delCGGCGGCGGCGGCGGCGGCGG p.Gly392_Gly398del disruptive_inframe_deletion Exon 1 of 20 ENST00000636930.2 NP_001361757.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARID1BENST00000636930.2 linkc.1173_1193delCGGCGGCGGCGGCGGCGGCGG p.Gly392_Gly398del disruptive_inframe_deletion Exon 1 of 20 2 NM_001374828.1 ENSP00000490491.2 Q8NFD5-3A0A6Q8NVI4

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
AF:
7.96e-7
AC:
1
AN:
1255596
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
617184
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
24704
American (AMR)
AF:
0.00
AC:
0
AN:
17064
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20426
East Asian (EAS)
AF:
0.0000362
AC:
1
AN:
27604
South Asian (SAS)
AF:
0.00
AC:
0
AN:
58586
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
42444
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5046
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1009008
Other (OTH)
AF:
0.00
AC:
0
AN:
50714
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
4.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs587779747; hg19: chr6-157099981; API