rs6846071

Variant names:

• chr4-101481058-T-G
• rs6846071
• ENST00000504592.5:c.-256+58400T>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]

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000504592.5	c.-256+58400T>G		intron_variant	Intron 2 of 20	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;