NM_017935.5:c.1900+2259T>G

Variant names:

• chr4-102032524-T-G
• rs1872701
• NM_017935.5:c.1900+2259T>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.1900+2259T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,908 control chromosomes in the GnomAD database, including 33,520 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 0.66 (33517 hom., cov: 31)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 5 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

ENSG00000251309 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017935.5. 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
	BANK1	NM_017935.5	MANE Select	c.1900+2259T>G		intron	N/A	NP_060405.5
	BANK1	NM_001083907.3		c.1810+2259T>G		intron	N/A	NP_001077376.3
	BANK1	NM_001127507.3		c.1501+2259T>G		intron	N/A	NP_001120979.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000322953.9	TSL:1 MANE Select	c.1900+2259T>G		intron	N/A	ENSP00000320509.4
	BANK1	ENST00000508653.5	TSL:1	c.1501+2259T>G		intron	N/A	ENSP00000422314.1
	BANK1	ENST00000504592.5	TSL:2	c.1855+2259T>G		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100004 AN: 151784 Hom.: 33487 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.683

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.659 AC: 100081 AN: 151902 Hom.: 33517 Cov.: 31 AF XY: 0.654 AC XY: 48549 AN XY: 74236

African (AFR) AF: 0.780 AC: 32302 AN: 41410

American (AMR) AF: 0.679 AC: 10365 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2308 AN: 3470

East Asian (EAS) AF: 0.637 AC: 3291 AN: 5164

South Asian (SAS) AF: 0.636 AC: 3059 AN: 4810

European-Finnish (FIN) AF: 0.533 AC: 5626 AN: 10550

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.602 AC: 40884 AN: 67928

Other (OTH) AF: 0.683 AC: 1443 AN: 2112

Alfa AF: 0.625 Hom.: 27475

Bravo AF: 0.675

Asia WGS AF: 0.667 AC: 2325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.9
DANN	Benign	0.78
PhyloP100		-0.22
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: rs1872701; hg19: chr4-102953681;