chr4-102052904-A-G

Variant names:

• chr4-102052904-A-G
• rs10516490
• NM_017935.5:c.1970-7307A>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.1970-7307A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,126 control chromosomes in the GnomAD database, including 8,037 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 (8037 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANK1	NM_017935.5	c.1970-7307A>G		intron_variant	Intron 11 of 16	ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3	c.1880-7307A>G		intron_variant	Intron 11 of 16		NP_001077376.3
BANK1	NM_001127507.3	c.1571-7307A>G		intron_variant	Intron 10 of 15		NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.1970-7307A>G		intron_variant	Intron 11 of 16	1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45846 AN: 152008 Hom.: 8041 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.301 AC: 45838 AN: 152126 Hom.: 8037 Cov.: 32 AF XY: 0.296 AC XY: 21999 AN XY: 74356

African (AFR) AF: 0.125 AC: 5178 AN: 41550

American (AMR) AF: 0.309 AC: 4720 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1564 AN: 5164

South Asian (SAS) AF: 0.440 AC: 2117 AN: 4816

European-Finnish (FIN) AF: 0.288 AC: 3048 AN: 10580

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26611 AN: 67954

Other (OTH) AF: 0.342 AC: 724 AN: 2114

Alfa AF: 0.371 Hom.: 8121

Bravo AF: 0.293

Asia WGS AF: 0.338 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.61
PhyloP100		-0.016
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: rs10516490; hg19: chr4-102974061;