rs4632664

Variant names:

• chr4-101771508-G-A
• rs4632664
• ENST00000504592.5:c.25+50075G>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000504592.5	c.25+50075G>A		intron_variant	Intron 5 of 20	2		ENSP00000421443.1

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;