rs11931658

Positions:

• chr4-101845735-T-C
• chr4-101845735-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017935.5(BANK1):​c.470-9300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,142 control chromosomes in the GnomAD database, including 7,427 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 (7427 hom., cov: 33)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANK1	NM_017935.5	c.470-9300T>C		intron_variant		ENST00000322953.9
BANK1	NM_001083907.3	c.380-9300T>C		intron_variant
BANK1	NM_001127507.3	c.71-9300T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000322953.9	c.470-9300T>C		intron_variant		1	NM_017935.5	P1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45866 AN: 152024 Hom.: 7429 Cov.: 33

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.302 AC: 45883 AN: 152142 Hom.: 7427 Cov.: 33 AF XY: 0.304 AC XY: 22618 AN XY: 74368

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.299

Alfa AF: 0.333 Hom.: 1066

Bravo AF: 0.281

Asia WGS AF: 0.220 AC: 766 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	5.0
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs11931658; hg19: chr4-102766892;