rs17199964

Variant names:

• chr4-101786634-G-A
• rs17199964
• ENST00000504592.5:c.26-43174G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-101786634-G-A
• chr4-101786634-G-C
• chr4-101786634-G-T

Variant summary

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

The ENST00000504592.5(BANK1):​c.26-43174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0473 in 146,024 control chromosomes in the GnomAD database, including 244 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 0.047 (244 hom., cov: 30)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000504592.5	c.26-43174G>A		intron_variant	Intron 5 of 20	2		ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 6908 AN: 146012 Hom.: 244 Cov.: 30

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0891

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.000607

Gnomad SAS AF: 0.00770

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0464

Gnomad NFE AF: 0.0716

Gnomad OTH AF: 0.0558

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

GnomAD4 genome AF: 0.0473 AC: 6903 AN: 146024 Hom.: 244 Cov.: 30 AF XY: 0.0452 AC XY: 3202 AN XY: 70858

Gnomad4 AFR AF: 0.0131

Gnomad4 AMR AF: 0.0580

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.000609

Gnomad4 SAS AF: 0.00774

Gnomad4 FIN AF: 0.0183

Gnomad4 NFE AF: 0.0716

Gnomad4 OTH AF: 0.0554

Alfa AF: 0.0135 Hom.: 11

Bravo AF: 0.0495

Asia WGS AF: 0.00925 AC: 32 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17199964; hg19: chr4-102707791;