rs2631268

Variant names:

• chr4-102027573-G-T
• rs2631268
• NM_017935.5:c.1594+2064G>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.1594+2064G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 150,640 control chromosomes in the GnomAD database, including 6,924 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 0.30 (6924 hom., cov: 31)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 7 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

ENSG00000251309 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANK1	NM_017935.5	c.1594+2064G>T		intron_variant	Intron 9 of 16	ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3	c.1504+2064G>T		intron_variant	Intron 9 of 16		NP_001077376.3
BANK1	NM_001127507.3	c.1195+2064G>T		intron_variant	Intron 8 of 15		NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.1594+2064G>T		intron_variant	Intron 9 of 16	1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45137 AN: 150524 Hom.: 6906 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.300 AC: 45185 AN: 150640 Hom.: 6924 Cov.: 31 AF XY: 0.303 AC XY: 22269 AN XY: 73496

African (AFR) AF: 0.301 AC: 12310 AN: 40960

American (AMR) AF: 0.393 AC: 5942 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1210 AN: 3460

East Asian (EAS) AF: 0.374 AC: 1917 AN: 5124

South Asian (SAS) AF: 0.308 AC: 1472 AN: 4776

European-Finnish (FIN) AF: 0.245 AC: 2497 AN: 10186

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18792 AN: 67700

Other (OTH) AF: 0.326 AC: 683 AN: 2098

Alfa AF: 0.287 Hom.: 26726

Bravo AF: 0.312

Asia WGS AF: 0.362 AC: 1257 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.8
DANN	Benign	0.58
PhyloP100		-0.012
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: rs2631268; hg19: chr4-102948730;