rs890448

chr4-101511545-C-T

Variant summary

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

The ENST00000504592.5(BANK1):c.-256+88887C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,976 control chromosomes in the GnomAD database, including 8,817 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 0.33 (8817 hom., cov: 32)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 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.-256+88887C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50012 AN: 151858 Hom.: 8811 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.329 AC: 50047 AN: 151976 Hom.: 8817 Cov.: 32 AF XY: 0.340 AC XY: 25283 AN XY: 74276

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.318

Alfa AF: 0.325 Hom.: 14496

Bravo AF: 0.328

Asia WGS AF: 0.521 AC: 1814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.88
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs890448; hg19: chr4-102432702;