rs4632664

Positions:

• chr4-101771508-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504592.5(BANK1):​c.25+50075G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0592 in 152,108 control chromosomes in the GnomAD database, including 356 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 0.059 (356 hom., cov: 32)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000504592.5	c.25+50075G>A		intron_variant		2		ENSP00000421443

Frequencies

GnomAD3 genomes AF: 0.0593 AC: 9011 AN: 151990 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0592 AC: 9002 AN: 152108 Hom.: 356 Cov.: 32 AF XY: 0.0599 AC XY: 4457 AN XY: 74352

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.0652

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0431

Gnomad4 FIN AF: 0.0932

Gnomad4 NFE AF: 0.0682

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0666 Hom.: 518

Bravo AF: 0.0562

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.9
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4632664; hg19: chr4-102692665;