rs2631267

Variant names:

• chr4-102027315-A-G
• rs2631267
• NM_017935.5:c.1594+1806A>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.1594+1806A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,182 control chromosomes in the GnomAD database, including 1,098 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 0.10 (1098 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 10 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANK1	NM_017935.5	c.1594+1806A>G		intron_variant	Intron 9 of 16	ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3	c.1504+1806A>G		intron_variant	Intron 9 of 16		NP_001077376.3
BANK1	NM_001127507.3	c.1195+1806A>G		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+1806A>G		intron_variant	Intron 9 of 16	1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15391 AN: 152064 Hom.: 1098 Cov.: 32

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.101 AC: 15396 AN: 152182 Hom.: 1098 Cov.: 32 AF XY: 0.106 AC XY: 7886 AN XY: 74422

African (AFR) AF: 0.0222 AC: 923 AN: 41566

American (AMR) AF: 0.200 AC: 3054 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3464

East Asian (EAS) AF: 0.193 AC: 1001 AN: 5174

South Asian (SAS) AF: 0.112 AC: 539 AN: 4824

European-Finnish (FIN) AF: 0.137 AC: 1448 AN: 10578

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.110 AC: 7506 AN: 67984

Other (OTH) AF: 0.118 AC: 249 AN: 2110

Alfa AF: 0.109 Hom.: 2440

Bravo AF: 0.104

Asia WGS AF: 0.138 AC: 481 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.039
DANN	Benign	0.32
PhyloP100		-1.6
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: rs2631267; hg19: chr4-102948472;