chr4-101871197-G-A

Position:

• chr4-101871197-G-A

Variant summary

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

The NM_017935.5(BANK1):​c.903+553G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,832 control chromosomes in the GnomAD database, including 1,445 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 0.12 (1445 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANK1	NM_017935.5	c.903+553G>A		intron_variant		ENST00000322953.9
BANK1	NM_001083907.3	c.813+553G>A		intron_variant
BANK1	NM_001127507.3	c.504+553G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000322953.9	c.903+553G>A		intron_variant		1	NM_017935.5	P1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18109 AN: 151714 Hom.: 1440 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0958

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.120 AC: 18152 AN: 151832 Hom.: 1445 Cov.: 32 AF XY: 0.122 AC XY: 9078 AN XY: 74180

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.0958

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.0977

Gnomad4 FIN AF: 0.0557

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0782 Hom.: 610

Bravo AF: 0.136

Asia WGS AF: 0.184 AC: 637 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
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: rs17031755; hg19: chr4-102792354;