rs12648641

Variant names:

• chr4-101738593-C-A
• rs12648641
• ENST00000504592.5:c.25+17160C>A

Variant summary

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

The ENST00000504592.5(BANK1):​c.25+17160C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,100 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 33)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 2 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

LOC107986297 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504592.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000504592.5	TSL:2	c.25+17160C>A		intron	N/A	ENSP00000421443.1	Q8NDB2-2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18542 AN: 151982 Hom.: 1286 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.122 AC: 18576 AN: 152100 Hom.: 1288 Cov.: 33 AF XY: 0.127 AC XY: 9443 AN XY: 74362

African (AFR) AF: 0.135 AC: 5601 AN: 41506

American (AMR) AF: 0.127 AC: 1945 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1406 AN: 5178

South Asian (SAS) AF: 0.152 AC: 735 AN: 4822

European-Finnish (FIN) AF: 0.138 AC: 1456 AN: 10576

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6751 AN: 67960

Other (OTH) AF: 0.123 AC: 259 AN: 2108

Alfa AF: 0.109 Hom.: 286

Bravo AF: 0.121

Asia WGS AF: 0.221 AC: 765 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.21
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12648641;

hg19: chr4-102659750;