rs7656409

Positions:

• chr4-101803248-A-G
• chr4-101803248-A-T

Variant summary

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

The ENST00000322953.9(BANK1):​c.70+12298A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,848 control chromosomes in the GnomAD database, including 23,437 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 0.55 (23437 hom., cov: 31)
• Consequence: BANK1 ENST00000322953.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

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 (SAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BANK1	NM_017935.5	c.70+12298A>G		intron_variant		ENST00000322953.9	NP_060405.5
BANK1	NM_001127507.3	c.70+12298A>G		intron_variant			NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.70+12298A>G		intron_variant		1	NM_017935.5	ENSP00000320509	P1
BANK1	ENST00000508653.5	c.70+12298A>G		intron_variant		1		ENSP00000422314
BANK1	ENST00000428908.5	c.70+12298A>G		intron_variant		5		ENSP00000412748
BANK1	ENST00000504592.5	c.26-26560A>G		intron_variant		2		ENSP00000421443

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84126 AN: 151730 Hom.: 23424 Cov.: 31

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.554 AC: 84179 AN: 151848 Hom.: 23437 Cov.: 31 AF XY: 0.551 AC XY: 40897 AN XY: 74214

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.568

Alfa AF: 0.545 Hom.: 3322

Bravo AF: 0.551

Asia WGS AF: 0.596 AC: 2072 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.51

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: rs7656409; hg19: chr4-102724405;