rs11097755

chr4-101788151-T-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000504592.5(BANK1):c.26-41657T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,956 control chromosomes in the GnomAD database, including 11,436 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 0.36 (11436 hom., cov: 31)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000504592.5	c.26-41657T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55435 AN: 151838 Hom.: 11435 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.365 AC: 55457 AN: 151956 Hom.: 11436 Cov.: 31 AF XY: 0.368 AC XY: 27358 AN XY: 74246

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.385

Alfa AF: 0.380 Hom.: 1075

Bravo AF: 0.350

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
Cadd	Benign	17
Dann	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11097755; hg19: chr4-102709308;