rs4699258

Variant names:

• chr4-101789531-G-A
• rs4699258
• ENST00000504592.5:c.26-40277G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-101789531-G-A
• chr4-101789531-G-C

Variant summary

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

The ENST00000504592.5(BANK1):​c.26-40277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,020 control chromosomes in the GnomAD database, including 12,164 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 0.38 (12164 hom., cov: 32)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000504592.5	c.26-40277G>A		intron_variant	Intron 5 of 20	2		ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57470 AN: 151902 Hom.: 12145 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.378 AC: 57532 AN: 152020 Hom.: 12164 Cov.: 32 AF XY: 0.374 AC XY: 27801 AN XY: 74330

African (AFR) AF: 0.585 AC: 24238 AN: 41446

American (AMR) AF: 0.273 AC: 4174 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1067 AN: 3466

East Asian (EAS) AF: 0.229 AC: 1186 AN: 5178

South Asian (SAS) AF: 0.177 AC: 853 AN: 4822

European-Finnish (FIN) AF: 0.338 AC: 3559 AN: 10542

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21446 AN: 67964

Other (OTH) AF: 0.332 AC: 700 AN: 2110

Alfa AF: 0.321 Hom.: 3890

Bravo AF: 0.384

Asia WGS AF: 0.252 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.4
DANN	Benign	0.39
PhyloP100		-0.065
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: rs4699258; hg19: chr4-102710688;