4-101866266-G-T

Variant summary

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

The NM_017935.5(BANK1):c.763+3602G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,966 control chromosomes in the GnomAD database, including 9,371 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 0.35 (9371 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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 (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANK1	NM_017935.5	c.763+3602G>T		intron_variant		ENST00000322953.9
BANK1	NM_001083907.3	c.673+3602G>T		intron_variant
BANK1	NM_001127507.3	c.364+3602G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000322953.9	c.763+3602G>T		intron_variant		1	NM_017935.5	P1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52430 AN: 151848 Hom.: 9373 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.345 AC: 52460 AN: 151966 Hom.: 9371 Cov.: 32 AF XY: 0.347 AC XY: 25776 AN XY: 74282

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.324

Alfa AF: 0.332 Hom.: 4068

Bravo AF: 0.331

Asia WGS AF: 0.227 AC: 789 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.67

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: rs4698977; hg19: chr4-102787423;