4-101933233-A-G

Variant names:

• chr4-101933233-A-G
• rs17208914
• NM_017935.5:c.1206+15044A>G

Variant summary

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

The NM_017935.5(BANK1):​c.1206+15044A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 150,628 control chromosomes in the GnomAD database, including 15,680 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 0.45 (15680 hom., cov: 29)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 10 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANK1	NM_017935.5	c.1206+15044A>G		intron_variant	Intron 7 of 16	ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3	c.1116+15044A>G		intron_variant	Intron 7 of 16		NP_001077376.3
BANK1	NM_001127507.3	c.807+15044A>G		intron_variant	Intron 6 of 15		NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.1206+15044A>G		intron_variant	Intron 7 of 16	1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68239 AN: 150510 Hom.: 15672 Cov.: 29

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.453 AC: 68291 AN: 150628 Hom.: 15680 Cov.: 29 AF XY: 0.452 AC XY: 33228 AN XY: 73508

African (AFR) AF: 0.447 AC: 18390 AN: 41146

American (AMR) AF: 0.454 AC: 6848 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1704 AN: 3448

East Asian (EAS) AF: 0.484 AC: 2448 AN: 5058

South Asian (SAS) AF: 0.543 AC: 2596 AN: 4782

European-Finnish (FIN) AF: 0.414 AC: 4340 AN: 10488

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30276 AN: 67354

Other (OTH) AF: 0.455 AC: 948 AN: 2082

Alfa AF: 0.457 Hom.: 42530

Bravo AF: 0.459

Asia WGS AF: 0.485 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.3
DANN	Benign	0.78
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17208914; hg19: chr4-102854390;