6-156777818-CGCGGCGGCGGCG-CGCG

Variant names:

• chr6-156777818-CGCGGCGGCG-C
• rs1046394316
• NM_001374828.1:c.150_158delGGCGGCGGC

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP3 BS1 BS2

The NM_001374828.1(ARID1B):​c.150_158delGGCGGCGGC​(p.Ala51_Ala53del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000248 in 1,011,732 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00025 (0 hom., cov: 30)
  • Exomes 𝑓: 0.00025 (0 hom.)
• Consequence: ARID1B NM_001374828.1 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28

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]

ENSG00000271551 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001374828.1
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000253 (36/142226) while in subpopulation EAS AF= 0.000414 (2/4832). AF 95% confidence interval is 0.000231. There are 0 homozygotes in gnomad4. There are 14 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 36 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1	c.150_158delGGCGGCGGC	p.Ala51_Ala53del	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.150_158delGGCGGCGGC	p.Ala51_Ala53del	disruptive_inframe_deletion	Exon 1 of 20	2	NM_001374828.1	ENSP00000490491.2

Frequencies

GnomAD3 genomes AF: 0.000253 AC: 36 AN: 142226 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.000152

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000275

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000414

Gnomad SAS AF: 0.000215

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000342

Gnomad OTH AF: 0.000512

GnomAD4 exome AF: 0.000247 AC: 215 AN: 869506 Hom.: 0 AF XY: 0.000227 AC XY: 92 AN XY: 404822

Gnomad4 AFR exome AF: 0.000295

Gnomad4 AMR exome AF: 0.000434

Gnomad4 ASJ exome AF: 0.000152

Gnomad4 EAS exome AF: 0.00244

Gnomad4 SAS exome AF: 0.000285

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000227

Gnomad4 OTH exome AF: 0.000268

GnomAD4 genome AF: 0.000253 AC: 36 AN: 142226 Hom.: 0 Cov.: 30 AF XY: 0.000203 AC XY: 14 AN XY: 69132

Gnomad4 AFR AF: 0.000152

Gnomad4 AMR AF: 0.000275

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000414

Gnomad4 SAS AF: 0.000215

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000342

Gnomad4 OTH AF: 0.000512

ClinVar

Not reported in ClinVar

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: rs1046394316; hg19: chr6-157098952;