rs2851318

Variant names:

• chr4-101994511-A-T
• rs2851318
• NM_017935.5:c.1207-27003A>T

Variant summary

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

The NM_017935.5(BANK1):​c.1207-27003A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 151,898 control chromosomes in the GnomAD database, including 49,381 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 0.80 (49381 hom., cov: 30)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 4 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:58860):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.874 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.1207-27003A>T		intron	N/A	NP_060405.5
	BANK1	NM_001083907.3		c.1117-27003A>T		intron	N/A	NP_001077376.3
	BANK1	NM_001127507.3		c.808-27003A>T		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.1207-27003A>T		intron	N/A	ENSP00000320509.4
	BANK1	ENST00000508653.5	TSL:1	c.808-27003A>T		intron	N/A	ENSP00000422314.1
	BANK1	ENST00000504592.5	TSL:2	c.1162-27003A>T		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121608 AN: 151782 Hom.: 49360 Cov.: 30

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.801 AC: 121676 AN: 151898 Hom.: 49381 Cov.: 30 AF XY: 0.799 AC XY: 59325 AN XY: 74240

African (AFR) AF: 0.685 AC: 28341 AN: 41396

American (AMR) AF: 0.733 AC: 11149 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2921 AN: 3468

East Asian (EAS) AF: 0.694 AC: 3576 AN: 5152

South Asian (SAS) AF: 0.730 AC: 3516 AN: 4814

European-Finnish (FIN) AF: 0.907 AC: 9587 AN: 10566

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59823 AN: 67962

Other (OTH) AF: 0.798 AC: 1687 AN: 2114

Alfa AF: 0.848 Hom.: 6731

Bravo AF: 0.786

Asia WGS AF: 0.710 AC: 2475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.30
PhyloP100		0.0
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: rs2851318; hg19: chr4-102915668;