rs1469019

Variant names:

• chr4-101837303-C-A
• rs1469019
• NM_017935.5:c.469+7097C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017935.5(BANK1):​c.469+7097C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 152,150 control chromosomes in the GnomAD database, including 609 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 0.070 (609 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 5 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.183 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	NM_017935.5	MANE Select	c.469+7097C>A		intron	N/A	NP_060405.5
	BANK1	NM_001083907.3		c.379+7097C>A		intron	N/A	NP_001077376.3	Q8NDB2-3
	BANK1	NM_001127507.3		c.71-17732C>A		intron	N/A	NP_001120979.3	Q8NDB2-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000322953.9	TSL:1 MANE Select	c.469+7097C>A		intron	N/A	ENSP00000320509.4	Q8NDB2-1
	BANK1	ENST00000508653.5	TSL:1	c.71-17732C>A		intron	N/A	ENSP00000422314.1	Q8NDB2-4
	BANK1	ENST00000504592.5	TSL:2	c.424+7097C>A		intron	N/A	ENSP00000421443.1	Q8NDB2-2

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10641 AN: 152032 Hom.: 603 Cov.: 32

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.0561

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.0700 AC: 10654 AN: 152150 Hom.: 609 Cov.: 32 AF XY: 0.0737 AC XY: 5485 AN XY: 74396

African (AFR) AF: 0.0163 AC: 677 AN: 41534

American (AMR) AF: 0.188 AC: 2876 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0998 AC: 346 AN: 3468

East Asian (EAS) AF: 0.129 AC: 666 AN: 5180

South Asian (SAS) AF: 0.0968 AC: 466 AN: 4814

European-Finnish (FIN) AF: 0.0561 AC: 592 AN: 10562

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0695 AC: 4725 AN: 68002

Other (OTH) AF: 0.0959 AC: 203 AN: 2116

Alfa AF: 0.0670 Hom.: 113

Bravo AF: 0.0768

Asia WGS AF: 0.126 AC: 436 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	12
DANN	Benign	0.60
PhyloP100		-0.70
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: rs1469019; hg19: chr4-102758460;