rs11944613

Variant names:

• chr4-101797638-A-G
• rs11944613
• NM_017935.5:c.70+6688A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017935.5(BANK1):​c.70+6688A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,038 control chromosomes in the GnomAD database, including 6,232 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 0.28 (6232 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990
• Publications: 7 publications found

Genes affected

BANK1 (HGNC:18233): (B cell scaffold protein with ankyrin repeats 1) The protein encoded by this gene is a B-cell-specific scaffold protein that functions in B-cell receptor-induced calcium mobilization from intracellular stores. This protein can also promote Lyn-mediated tyrosine phosphorylation of inositol 1,4,5-trisphosphate receptors. Polymorphisms in this gene are associated with susceptibility to systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

BANK1 Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017935.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	NM_017935.5	MANE Select	c.70+6688A>G		intron	N/A	NP_060405.5
	BANK1	NM_001127507.3		c.70+6688A>G		intron	N/A	NP_001120979.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000322953.9	TSL:1 MANE Select	c.70+6688A>G		intron	N/A	ENSP00000320509.4
	BANK1	ENST00000508653.5	TSL:1	c.70+6688A>G		intron	N/A	ENSP00000422314.1
	BANK1	ENST00000504592.5	TSL:2	c.26-32170A>G		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42657 AN: 151920 Hom.: 6233 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.267

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.281 AC: 42673 AN: 152038 Hom.: 6232 Cov.: 32 AF XY: 0.279 AC XY: 20737 AN XY: 74324

African (AFR) AF: 0.224 AC: 9312 AN: 41494

American (AMR) AF: 0.244 AC: 3731 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1374 AN: 5166

South Asian (SAS) AF: 0.155 AC: 745 AN: 4818

European-Finnish (FIN) AF: 0.341 AC: 3601 AN: 10568

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21931 AN: 67942

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.309 Hom.: 32162

Bravo AF: 0.273

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.83
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11944613; hg19: chr4-102718795;