4-101786634-G-A

Variant names:

• chr4-101786634-G-A
• rs17199964
• ENST00000504592.5:c.26-43174G>A

Variant summary

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

The ENST00000504592.5(BANK1):​c.26-43174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0473 in 146,024 control chromosomes in the GnomAD database, including 244 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 0.047 (244 hom., cov: 30)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504592.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000504592.5	TSL:2	c.26-43174G>A		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 6908 AN: 146012 Hom.: 244 Cov.: 30

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0891

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.000607

Gnomad SAS AF: 0.00770

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0464

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.0558

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

GnomAD4 genome AF: 0.0473 AC: 6903 AN: 146024 Hom.: 244 Cov.: 30 AF XY: 0.0452 AC XY: 3202 AN XY: 70858

African (AFR) AF: 0.0131 AC: 510 AN: 38896

American (AMR) AF: 0.0580 AC: 852 AN: 14686

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 317 AN: 3440

East Asian (EAS) AF: 0.000609 AC: 3 AN: 4926

South Asian (SAS) AF: 0.00774 AC: 35 AN: 4520

European-Finnish (FIN) AF: 0.0183 AC: 165 AN: 9036

Middle Eastern (MID) AF: 0.0396 AC: 11 AN: 278

European-Non Finnish (NFE) AF: 0.0716 AC: 4816 AN: 67288

Other (OTH) AF: 0.0554 AC: 114 AN: 2056

Alfa AF: 0.0602 Hom.: 462

Bravo AF: 0.0495

Asia WGS AF: 0.00925 AC: 32 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		-0.097
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17199964; hg19: chr4-102707791;