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GeneBe

6-156777701-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001374828.1(ARID1B):c.21G>A(p.Ala7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 137,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00029 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00041 ( 0 hom. )

Consequence

ARID1B
NM_001374828.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.13
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-156777701-G-A is Benign according to our data. Variant chr6-156777701-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657049.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.13 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000288 (39/135550) while in subpopulation NFE AF= 0.000406 (24/59148). AF 95% confidence interval is 0.000279. There are 0 homozygotes in gnomad4. There are 15 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 39 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARID1BNM_001374828.1 linkuse as main transcriptc.21G>A p.Ala7= synonymous_variant 1/20 ENST00000636930.2
LOC115308161NR_163974.1 linkuse as main transcriptn.274-270C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARID1BENST00000636930.2 linkuse as main transcriptc.21G>A p.Ala7= synonymous_variant 1/202 NM_001374828.1 A2Q8NFD5-3
ENST00000603191.2 linkuse as main transcriptn.178-270C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000288
AC:
39
AN:
135550
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000503
Gnomad AMI
AF:
0.00980
Gnomad AMR
AF:
0.000217
Gnomad ASJ
AF:
0.000329
Gnomad EAS
AF:
0.000204
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000406
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000408
AC:
1
AN:
2448
Hom.:
0
Cov.:
0
AF XY:
0.000873
AC XY:
1
AN XY:
1146
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000462
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000288
AC:
39
AN:
135550
Hom.:
0
Cov.:
31
AF XY:
0.000227
AC XY:
15
AN XY:
65962
show subpopulations
Gnomad4 AFR
AF:
0.0000503
Gnomad4 AMR
AF:
0.000217
Gnomad4 ASJ
AF:
0.000329
Gnomad4 EAS
AF:
0.000204
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000406
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00329
Hom.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2023ARID1B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
Cadd
Benign
14
Dann
Benign
0.85
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.0

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs186825263; hg19: chr6-157098835; API