rs13129744

Variant names:

• chr4-101835574-T-C
• rs13129744
• NM_017935.5:c.469+5368T>C

Variant summary

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

The NM_017935.5(BANK1):​c.469+5368T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,178 control chromosomes in the GnomAD database, including 4,421 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 0.23 (4421 hom., cov: 33)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANK1	NM_017935.5	c.469+5368T>C		intron_variant	Intron 2 of 16	ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3	c.379+5368T>C		intron_variant	Intron 2 of 16		NP_001077376.3
BANK1	NM_001127507.3	c.71-19461T>C		intron_variant	Intron 1 of 15		NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.469+5368T>C		intron_variant	Intron 2 of 16	1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34891 AN: 152060 Hom.: 4427 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.229 AC: 34888 AN: 152178 Hom.: 4421 Cov.: 33 AF XY: 0.229 AC XY: 17038 AN XY: 74400

African (AFR) AF: 0.138 AC: 5725 AN: 41530

American (AMR) AF: 0.196 AC: 3002 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1062 AN: 3472

East Asian (EAS) AF: 0.165 AC: 855 AN: 5174

South Asian (SAS) AF: 0.176 AC: 848 AN: 4822

European-Finnish (FIN) AF: 0.321 AC: 3400 AN: 10582

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19303 AN: 67998

Other (OTH) AF: 0.226 AC: 478 AN: 2112

Alfa AF: 0.267 Hom.: 2975

Bravo AF: 0.214

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.75
PhyloP100		-0.0070
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: rs13129744; hg19: chr4-102756731;