rs4699258

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000504592.5	c.26-40277G>A		intron_variant		2

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

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.332

Alfa AF: 0.167 Hom.: 261

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4699258; hg19: chr4-102710688;