6-156777692-G-GGCA

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3 BP6_Moderate BA1

The NM_001374828.1(ARID1B):c.18_20dup(p.Ala13dup) variant causes a inframe insertion change. The variant allele was found at a frequency of 0.0504 in 148,240 control chromosomes in the GnomAD database, including 237 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.050 (233 hom., cov: 30)
  • Exomes 𝑓: 0.050 (4 hom.)
• Consequence: ARID1B NM_001374828.1 inframe_insertion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.54

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001374828.1
• BP6: Variant 6-156777692-G-GGCA is Benign according to our data. Variant chr6-156777692-G-GGCA is described in ClinVar as [Benign]. Clinvar id is 1282345.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.075 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID1B	NM_001374828.1	c.18_20dup	p.Ala13dup	inframe_insertion	1/20	ENST00000636930.2
LOC115308161	NR_163974.1	n.274-262_274-261insTGC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID1B	ENST00000636930.2	c.18_20dup	p.Ala13dup	inframe_insertion	1/20	2	NM_001374828.1	A2
	ENST00000603191.2	n.178-262_178-261insTGC		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7357 AN: 145842 Hom.: 233 Cov.: 30

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.000201

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0514

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0767

Gnomad OTH AF: 0.0553

GnomAD4 exome AF: 0.0501 AC: 118 AN: 2356 Hom.: 4 Cov.: 0 AF XY: 0.0470 AC XY: 52 AN XY: 1106

Gnomad4 AFR exome AF: 0.0526

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0981

Gnomad4 NFE exome AF: 0.0460

Gnomad4 OTH exome AF: 0.0227

GnomAD4 genome AF: 0.0504 AC: 7356 AN: 145884 Hom.: 233 Cov.: 30 AF XY: 0.0493 AC XY: 3497 AN XY: 70976

Gnomad4 AFR AF: 0.0142

Gnomad4 AMR AF: 0.0446

Gnomad4 ASJ AF: 0.0704

Gnomad4 EAS AF: 0.000202

Gnomad4 SAS AF: 0.0405

Gnomad4 FIN AF: 0.0514

Gnomad4 NFE AF: 0.0768

Gnomad4 OTH AF: 0.0554

Asia WGS AF: 0.0200 AC: 67 AN: 3236

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 26, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs557453022; hg19: chr6-157098826;