rs7685012

Positions:

• chr4-102027834-T-C

Variant summary

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

The NM_017935.5(BANK1):​c.1595-2126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,214 control chromosomes in the GnomAD database, including 690 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 0.084 (690 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANK1	NM_017935.5	c.1595-2126T>C		intron_variant		ENST00000322953.9
BANK1	NM_001083907.3	c.1505-2126T>C		intron_variant
BANK1	NM_001127507.3	c.1196-2126T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000322953.9	c.1595-2126T>C		intron_variant		1	NM_017935.5	P1
	ENST00000505091.1	n.396+4375A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12796 AN: 152096 Hom.: 687 Cov.: 32

Gnomad AFR AF: 0.0250

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0991

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00846

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0766

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0841 AC: 12802 AN: 152214 Hom.: 690 Cov.: 32 AF XY: 0.0831 AC XY: 6187 AN XY: 74428

Gnomad4 AFR AF: 0.0249

Gnomad4 AMR AF: 0.0993

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.00867

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0766

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.107

Alfa AF: 0.110 Hom.: 972

Bravo AF: 0.0821

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7685012; hg19: chr4-102948991;