rs7700191

Variant names:

• chr4-101668126-G-A
• rs7700191
• ENST00000504592.5:c.-255-1277G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-101668126-G-A
• chr4-101668126-G-C
• chr4-101668126-G-T

Variant summary

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

The ENST00000504592.5(BANK1):​c.-255-1277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 151,792 control chromosomes in the GnomAD database, including 310 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 0.056 (310 hom., cov: 32)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0806 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.-255-1277G>A		intron_variant	Intron 2 of 20	2		ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8476 AN: 151676 Hom.: 310 Cov.: 32

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.0375

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

GnomAD4 genome AF: 0.0558 AC: 8472 AN: 151792 Hom.: 310 Cov.: 32 AF XY: 0.0555 AC XY: 4113 AN XY: 74138

Gnomad4 AFR AF: 0.0142

Gnomad4 AMR AF: 0.0461

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0824

Gnomad4 OTH AF: 0.0371

Alfa AF: 0.0662 Hom.: 209

Bravo AF: 0.0501

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7700191; hg19: chr4-102589283;