4-101787078-C-T

Variant names:

• chr4-101787078-C-T
• rs4371620
• ENST00000504592.5:c.26-42730C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504592.5(BANK1):​c.26-42730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,262 control chromosomes in the GnomAD database, including 51,861 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 0.82 (51861 hom., cov: 34)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.866 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.26-42730C>T		intron_variant	Intron 5 of 20	2		ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125381 AN: 152144 Hom.: 51826 Cov.: 34

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.824 AC: 125477 AN: 152262 Hom.: 51861 Cov.: 34 AF XY: 0.824 AC XY: 61358 AN XY: 74448

African (AFR) AF: 0.868 AC: 36087 AN: 41562

American (AMR) AF: 0.861 AC: 13175 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2689 AN: 3470

East Asian (EAS) AF: 0.783 AC: 4059 AN: 5184

South Asian (SAS) AF: 0.888 AC: 4290 AN: 4830

European-Finnish (FIN) AF: 0.784 AC: 8305 AN: 10590

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54139 AN: 68004

Other (OTH) AF: 0.822 AC: 1737 AN: 2112

Alfa AF: 0.805 Hom.: 74760

Bravo AF: 0.831

Asia WGS AF: 0.836 AC: 2906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.64
PhyloP100		-0.25
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: rs4371620; hg19: chr4-102708235;