ENST00000504592.5:c.-256+58400T>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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]

BANK1 Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504592.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000504592.5	TSL:2	c.-256+58400T>G		intron	N/A	ENSP00000421443.1	Q8NDB2-2

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

African (AFR) AF: 0.465 AC: 19241 AN: 41404

American (AMR) AF: 0.0706 AC: 1078 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3468

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5180

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4822

European-Finnish (FIN) AF: 0.0177 AC: 188 AN: 10614

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.00965 AC: 656 AN: 67996

Other (OTH) AF: 0.112 AC: 236 AN: 2112

Alfa AF: 0.0558 Hom.: 4572

Bravo AF: 0.164

Asia WGS AF: 0.0500 AC: 173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.19
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6846071; hg19: chr4-102402215;