chr4-101902269-C-T

Variant names:

• chr4-101902269-C-T
• rs7694392
• NM_017935.5:c.1009+6859C>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.1009+6859C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,160 control chromosomes in the GnomAD database, including 49,257 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 (49257 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.883 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.1009+6859C>T		intron	N/A	NP_060405.5
	BANK1	NM_001083907.3		c.919+6859C>T		intron	N/A	NP_001077376.3
	BANK1	NM_001127507.3		c.610+6859C>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.1009+6859C>T		intron	N/A	ENSP00000320509.4
	BANK1	ENST00000508653.5	TSL:1	c.610+6859C>T		intron	N/A	ENSP00000422314.1
	BANK1	ENST00000504592.5	TSL:2	c.964+6859C>T		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121176 AN: 152042 Hom.: 49249 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.797 AC: 121234 AN: 152160 Hom.: 49257 Cov.: 32 AF XY: 0.794 AC XY: 59059 AN XY: 74404

African (AFR) AF: 0.656 AC: 27202 AN: 41474

American (AMR) AF: 0.732 AC: 11191 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2930 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3345 AN: 5176

South Asian (SAS) AF: 0.741 AC: 3576 AN: 4824

European-Finnish (FIN) AF: 0.924 AC: 9797 AN: 10598

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60459 AN: 68006

Other (OTH) AF: 0.786 AC: 1662 AN: 2114

Alfa AF: 0.855 Hom.: 50044

Bravo AF: 0.778

Asia WGS AF: 0.684 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.098
DANN	Benign	0.43
PhyloP100		-3.5
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: rs7694392; hg19: chr4-102823426;