rs2112139

Positions:

• chr4-101962268-T-C
• chr4-101962268-T-G

Variant summary

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

The NM_017935.5(BANK1):​c.1206+44079T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,050 control chromosomes in the GnomAD database, including 50,227 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 0.81 (50227 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BANK1	NM_017935.5	c.1206+44079T>C		intron_variant		ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3	c.1116+44079T>C		intron_variant			NP_001077376.3
BANK1	NM_001127507.3	c.807+44079T>C		intron_variant			NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.1206+44079T>C		intron_variant		1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122727 AN: 151932 Hom.: 50201 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.903

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.808 AC: 122800 AN: 152050 Hom.: 50227 Cov.: 32 AF XY: 0.804 AC XY: 59802 AN XY: 74340

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.883

Gnomad4 OTH AF: 0.794

Alfa AF: 0.865 Hom.: 77146

Bravo AF: 0.792

Asia WGS AF: 0.679 AC: 2367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.45

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: rs2112139; hg19: chr4-102883425;