rs10516490

chr4-102052904-A-G

Variant summary

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

The NM_017935.5(BANK1):c.1970-7307A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,126 control chromosomes in the GnomAD database, including 8,037 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 0.30 (8037 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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 (SAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANK1	NM_017935.5	c.1970-7307A>G		intron_variant		ENST00000322953.9
BANK1	NM_001083907.3	c.1880-7307A>G		intron_variant
BANK1	NM_001127507.3	c.1571-7307A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000322953.9	c.1970-7307A>G		intron_variant		1	NM_017935.5	P1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45846 AN: 152008 Hom.: 8041 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.301 AC: 45838 AN: 152126 Hom.: 8037 Cov.: 32 AF XY: 0.296 AC XY: 21999 AN XY: 74356

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.342

Alfa AF: 0.376 Hom.: 6136

Bravo AF: 0.293

Asia WGS AF: 0.338 AC: 1179 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	0.61

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: rs10516490; hg19: chr4-102974061;