ENST00000504592.5:c.26-41657T>C

Variant names:

• chr4-101788151-T-C
• rs11097755
• ENST00000504592.5:c.26-41657T>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000504592.5(BANK1):​c.26-41657T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,956 control chromosomes in the GnomAD database, including 11,436 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 0.36 (11436 hom., cov: 31)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841
• Publications: 6 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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504592.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000504592.5	TSL:2	c.26-41657T>C		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55435 AN: 151838 Hom.: 11435 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.365 AC: 55457 AN: 151956 Hom.: 11436 Cov.: 31 AF XY: 0.368 AC XY: 27358 AN XY: 74246

African (AFR) AF: 0.157 AC: 6514 AN: 41480

American (AMR) AF: 0.421 AC: 6425 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3466

East Asian (EAS) AF: 0.453 AC: 2336 AN: 5154

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4808

European-Finnish (FIN) AF: 0.464 AC: 4898 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30238 AN: 67926

Other (OTH) AF: 0.385 AC: 810 AN: 2104

Alfa AF: 0.424 Hom.: 22295

Bravo AF: 0.350

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Benign	17
DANN	Benign	0.71
PhyloP100		0.84
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11097755; hg19: chr4-102709308;