rs747790383
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr6-156778889-CGGAGGAGGAGGAGGA-C
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGAGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
- chr6-156778889-CGGAGGAGGAGGAGGA-CGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP3BS2_Supporting
The NM_001374828.1(ARID1B):c.1220_1234delGAGGAGGAGGAGGAG(p.Gly407_Gly411del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000512 in 1,366,536 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. Synonymous variant affecting the same amino acid position (i.e. G407G) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000049 ( 0 hom. )
Consequence
ARID1B
NM_001374828.1 disruptive_inframe_deletion
NM_001374828.1 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.18
Publications
0 publications found
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 syndromeInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina, ClinGen
- Coffin-Siris syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001374828.1
BS2
High AC in GnomAdExome4 at 6 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ARID1B | NM_001374828.1 | c.1220_1234delGAGGAGGAGGAGGAG | p.Gly407_Gly411del | 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| ARID1B | ENST00000636930.2 | c.1220_1234delGAGGAGGAGGAGGAG | p.Gly407_Gly411del | disruptive_inframe_deletion | Exon 1 of 20 | 2 | NM_001374828.1 | ENSP00000490491.2 |
Frequencies
GnomAD3 genomes 0.00000699 AC: 1AN: 142982Hom.: 0 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
142982
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000490 AC: 6AN: 1223554Hom.: 0 AF XY: 0.00000501 AC XY: 3AN XY: 599384 show subpopulations
GnomAD4 exome
AF:
AC:
6
AN:
1223554
Hom.:
AF XY:
AC XY:
3
AN XY:
599384
show subpopulations
African (AFR)
AF:
AC:
0
AN:
23958
American (AMR)
AF:
AC:
2
AN:
14566
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18616
East Asian (EAS)
AF:
AC:
0
AN:
27064
South Asian (SAS)
AF:
AC:
0
AN:
52790
European-Finnish (FIN)
AF:
AC:
0
AN:
40134
Middle Eastern (MID)
AF:
AC:
0
AN:
4406
European-Non Finnish (NFE)
AF:
AC:
4
AN:
992596
Other (OTH)
AF:
AC:
0
AN:
49424
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000699 AC: 1AN: 142982Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 69712 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
142982
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
69712
show subpopulations
African (AFR)
AF:
AC:
0
AN:
38842
American (AMR)
AF:
AC:
1
AN:
14528
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3376
East Asian (EAS)
AF:
AC:
0
AN:
4706
South Asian (SAS)
AF:
AC:
0
AN:
4466
European-Finnish (FIN)
AF:
AC:
0
AN:
9258
Middle Eastern (MID)
AF:
AC:
0
AN:
270
European-Non Finnish (NFE)
AF:
AC:
0
AN:
64724
Other (OTH)
AF:
AC:
0
AN:
1968
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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