rs1554248236

Variant names:

• chr6-156779412-C-A
• NM_001374828.1:c.1732C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-156779412-C-A
• chr6-156779412-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001374828.1(ARID1B):​c.1732C>A​(p.Gln578Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000000762 in 1,312,740 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 7.6e-7 (0 hom.)
• Consequence: ARID1B NM_001374828.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.27

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.26568985).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARID1B	NM_001374828.1	c.1732C>A	p.Gln578Lys	missense_variant	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.1732C>A	p.Gln578Lys	missense_variant	Exon 1 of 20	2	NM_001374828.1	ENSP00000490491.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 7.62e-7 AC: 1 AN: 1312740 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 653162

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: 0.0000192

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.46
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Uncertain	24
DANN	Benign	0.96
DEOGEN2	Benign	0.025	.;T;.;.;.;.
Eigen	Benign	-0.093
Eigen_PC	Benign	-0.067
FATHMM_MKL	Benign	0.67	D
LIST_S2	Benign	0.76	T;T;T;T;T;T
M_CAP	Pathogenic	0.54	D
MetaRNN	Benign	0.27	T;T;T;T;T;T
MetaSVM	Benign	-0.81	T
MutationAssessor	Benign	1.6	.;L;L;L;.;.
PrimateAI	Pathogenic	0.92	D
PROVEAN	Uncertain	-2.9	D;N;.;.;.;.
REVEL	Benign	0.14
Sift	Pathogenic	0.0	D;T;.;.;.;.
Sift4G	Benign	0.53	.;T;.;.;.;.
Polyphen		0.61, 0.73	.;P;.;P;.;.
Vest4		0.21
MutPred		0.34		.;Gain of methylation at Q495 (P = 1e-04);Gain of methylation at Q495 (P = 1e-04);Gain of methylation at Q495 (P = 1e-04);.;.;
MVP		0.44
MPC		0.82
ClinPred		0.89	D
GERP RS		3.0
Varity_R		0.31
gMVP		0.23

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-157100546;