chr4-102032524-T-G

Position:

• chr4-102032524-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.1900+2259T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,908 control chromosomes in the GnomAD database, including 33,520 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 0.66 (33517 hom., cov: 31)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

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]

ENSG00000251309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BANK1	NM_017935.5	c.1900+2259T>G		intron_variant		ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3	c.1810+2259T>G		intron_variant			NP_001077376.3
BANK1	NM_001127507.3	c.1501+2259T>G		intron_variant			NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.1900+2259T>G		intron_variant		1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100004 AN: 151784 Hom.: 33487 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.683

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.659 AC: 100081 AN: 151902 Hom.: 33517 Cov.: 31 AF XY: 0.654 AC XY: 48549 AN XY: 74236

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.683

Alfa AF: 0.614 Hom.: 19995

Bravo AF: 0.675

Asia WGS AF: 0.667 AC: 2325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.9
DANN	Benign	0.78

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: rs1872701; hg19: chr4-102953681;