rs4522865

Variant names:

• chr4-101794731-G-A
• rs4522865
• NM_017935.5:c.70+3781G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-101794731-G-A
• chr4-101794731-G-C
• chr4-101794731-G-T

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+3781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,870 control chromosomes in the GnomAD database, including 29,472 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 0.62 (29472 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 22 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANK1	NM_017935.5	c.70+3781G>A		intron_variant	Intron 1 of 16	ENST00000322953.9	NP_060405.5
BANK1	NM_001127507.3	c.70+3781G>A		intron_variant	Intron 1 of 15		NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.70+3781G>A		intron_variant	Intron 1 of 16	1	NM_017935.5	ENSP00000320509.4
BANK1	ENST00000508653.5	c.70+3781G>A		intron_variant	Intron 1 of 14	1		ENSP00000422314.1
BANK1	ENST00000504592.5	c.26-35077G>A		intron_variant	Intron 5 of 20	2		ENSP00000421443.1
BANK1	ENST00000428908.5	c.70+3781G>A		intron_variant	Intron 1 of 15	5		ENSP00000412748.1

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93444 AN: 151754 Hom.: 29446 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.616 AC: 93520 AN: 151870 Hom.: 29472 Cov.: 32 AF XY: 0.611 AC XY: 45364 AN XY: 74224

African (AFR) AF: 0.749 AC: 31030 AN: 41454

American (AMR) AF: 0.525 AC: 8007 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1973 AN: 3468

East Asian (EAS) AF: 0.580 AC: 2996 AN: 5164

South Asian (SAS) AF: 0.701 AC: 3381 AN: 4826

European-Finnish (FIN) AF: 0.512 AC: 5400 AN: 10550

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38693 AN: 67832

Other (OTH) AF: 0.607 AC: 1281 AN: 2112

Alfa AF: 0.589 Hom.: 49855

Bravo AF: 0.622

Asia WGS AF: 0.605 AC: 2098 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		-0.38
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: rs4522865; hg19: chr4-102715888;