4-101511545-C-T

Variant names:

• chr4-101511545-C-T
• rs890448
• ENST00000504592.5:c.-256+88887C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.89).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000504592.5	c.-256+88887C>T		intron_variant	Intron 2 of 20	2		ENSP00000421443.1

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

African (AFR) AF: 0.233 AC: 9666 AN: 41476

American (AMR) AF: 0.437 AC: 6661 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3466

East Asian (EAS) AF: 0.573 AC: 2952 AN: 5148

South Asian (SAS) AF: 0.439 AC: 2119 AN: 4824

European-Finnish (FIN) AF: 0.433 AC: 4567 AN: 10548

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21856 AN: 67936

Other (OTH) AF: 0.318 AC: 672 AN: 2116

Alfa AF: 0.325 Hom.: 33429

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
PhyloP100		-0.39
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: rs890448; hg19: chr4-102432702;