6-156777698-AGCGGCGGCGGCGGCG-AGCGGCGGCGGCGGCGGCGGCG

Variant names:

• chr6-156777698-A-AGCGGCG
• rs1046451353
• NM_001374828.1:c.37_42dupGCGGCG

Variant summary

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

The NM_001374828.1(ARID1B):​c.37_42dupGCGGCG​(p.Ala13_Ala14dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000508 in 143,582 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 0.00051 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ARID1B NM_001374828.1 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

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 afr. gnomad4 allele frequency = 0.000508 (73/143582) while in subpopulation AFR AF= 0.000925 (37/39986). AF 95% confidence interval is 0.000689. There are 0 homozygotes in gnomad4. There are 38 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 73 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1	c.37_42dupGCGGCG	p.Ala13_Ala14dup	conservative_inframe_insertion	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.37_42dupGCGGCG	p.Ala13_Ala14dup	conservative_inframe_insertion	Exon 1 of 20	2	NM_001374828.1	ENSP00000490491.2

Frequencies

GnomAD3 genomes AF: 0.000509 AC: 73 AN: 143530 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000927

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000412

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000630

Gnomad SAS AF: 0.000218

Gnomad FIN AF: 0.000123

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000384

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 3162 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1498

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000508 AC: 73 AN: 143582 Hom.: 0 Cov.: 31 AF XY: 0.000544 AC XY: 38 AN XY: 69816

Gnomad4 AFR AF: 0.000925

Gnomad4 AMR AF: 0.000412

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000633

Gnomad4 SAS AF: 0.000218

Gnomad4 FIN AF: 0.000123

Gnomad4 NFE AF: 0.000384

Gnomad4 OTH AF: 0.00

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: rs1046451353; hg19: chr6-157098832;