chr6-156940339-C-G

Position:

• chr6-156940339-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001374828.1(ARID1B):​c.2247+4763C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,084 control chromosomes in the GnomAD database, including 5,233 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (5233 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ARID1B NM_001374828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.995

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARID1B	NM_001374828.1	c.2247+4763C>G		intron_variant		ENST00000636930.2	NP_001361757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARID1B	ENST00000636930.2	c.2247+4763C>G		intron_variant		2	NM_001374828.1	ENSP00000490491.2

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32715 AN: 151964 Hom.: 5214 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.216 AC: 32780 AN: 152082 Hom.: 5233 Cov.: 33 AF XY: 0.215 AC XY: 16006 AN XY: 74322

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.210

Alfa AF: 0.0554 Hom.: 65

Bravo AF: 0.224

Asia WGS AF: 0.256 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6901717; hg19: chr6-157261473;