chr4-101804916-A-G

Variant names:

• chr4-101804916-A-G
• rs6833249
• NM_017935.5:c.70+13966A>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.70+13966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,186 control chromosomes in the GnomAD database, including 61,822 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 0.90 (61822 hom., cov: 31)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 11 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 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.70+13966A>G		intron	N/A	NP_060405.5
	BANK1	NM_001127507.3		c.70+13966A>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.70+13966A>G		intron	N/A	ENSP00000320509.4
	BANK1	ENST00000508653.5	TSL:1	c.70+13966A>G		intron	N/A	ENSP00000422314.1
	BANK1	ENST00000504592.5	TSL:2	c.26-24892A>G		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136700 AN: 152068 Hom.: 61775 Cov.: 31

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.899 AC: 136802 AN: 152186 Hom.: 61822 Cov.: 31 AF XY: 0.893 AC XY: 66412 AN XY: 74390

African (AFR) AF: 0.977 AC: 40604 AN: 41562

American (AMR) AF: 0.771 AC: 11776 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3089 AN: 3464

East Asian (EAS) AF: 0.849 AC: 4396 AN: 5176

South Asian (SAS) AF: 0.864 AC: 4164 AN: 4820

European-Finnish (FIN) AF: 0.852 AC: 9005 AN: 10570

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60842 AN: 68000

Other (OTH) AF: 0.877 AC: 1848 AN: 2108

Alfa AF: 0.891 Hom.: 129671

Bravo AF: 0.897

Asia WGS AF: 0.838 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.38
PhyloP100		-1.3
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: rs6833249; hg19: chr4-102726073;