4-101882879-G-A

Variant names:

• chr4-101882879-G-A
• rs13137047
• NM_017935.5:c.903+12235G>A

Variant summary

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

The NM_017935.5(BANK1):​c.903+12235G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 150,900 control chromosomes in the GnomAD database, including 636 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 0.076 (636 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• 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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	NM_017935.5	MANE Select	c.903+12235G>A		intron	N/A	NP_060405.5
	BANK1	NM_001083907.3		c.813+12235G>A		intron	N/A	NP_001077376.3	Q8NDB2-3
	BANK1	NM_001127507.3		c.504+12235G>A		intron	N/A	NP_001120979.3	Q8NDB2-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000322953.9	TSL:1 MANE Select	c.903+12235G>A		intron	N/A	ENSP00000320509.4	Q8NDB2-1
	BANK1	ENST00000508653.5	TSL:1	c.504+12235G>A		intron	N/A	ENSP00000422314.1	Q8NDB2-4
	BANK1	ENST00000504592.5	TSL:2	c.858+12235G>A		intron	N/A	ENSP00000421443.1	Q8NDB2-2

Frequencies

GnomAD3 genomes AF: 0.0757 AC: 11419 AN: 150784 Hom.: 635 Cov.: 32

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0946

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0758 AC: 11436 AN: 150900 Hom.: 636 Cov.: 32 AF XY: 0.0796 AC XY: 5873 AN XY: 73808

African (AFR) AF: 0.0391 AC: 1576 AN: 40302

American (AMR) AF: 0.186 AC: 2835 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0946 AC: 328 AN: 3468

East Asian (EAS) AF: 0.184 AC: 951 AN: 5178

South Asian (SAS) AF: 0.0928 AC: 447 AN: 4818

European-Finnish (FIN) AF: 0.0553 AC: 586 AN: 10594

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0647 AC: 4397 AN: 67986

Other (OTH) AF: 0.104 AC: 219 AN: 2110

Alfa AF: 0.0755 Hom.: 307

Bravo AF: 0.0831

Asia WGS AF: 0.132 AC: 456 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.81
PhyloP100		-0.092
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: rs13137047; hg19: chr4-102804036;