rs6846071

Positions:

• chr4-101481058-T-G

Variant summary

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

The ENST00000504592.5(BANK1):​c.-256+58400T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,070 control chromosomes in the GnomAD database, including 4,591 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 0.14 (4591 hom., cov: 31)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

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]

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101481058T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000504592.5	c.-256+58400T>G		intron_variant		2		ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21756 AN: 151952 Hom.: 4569 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0177

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.00965

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.144 AC: 21828 AN: 152070 Hom.: 4591 Cov.: 31 AF XY: 0.139 AC XY: 10372 AN XY: 74386

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.0706

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0177

Gnomad4 NFE AF: 0.00965

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0374 Hom.: 846

Bravo AF: 0.164

Asia WGS AF: 0.0500 AC: 173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6846071; hg19: chr4-102402215;