rs10516483

Positions:

• chr4-101870748-C-G

Variant summary

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

The NM_017935.5(BANK1):​c.903+104C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 1,310,130 control chromosomes in the GnomAD database, including 154,402 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 0.55 (24466 hom., cov: 31)
  • Exomes 𝑓: 0.47 (129936 hom.)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

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 = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANK1	NM_017935.5	c.903+104C>G		intron_variant		ENST00000322953.9
BANK1	NM_001083907.3	c.813+104C>G		intron_variant
BANK1	NM_001127507.3	c.504+104C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000322953.9	c.903+104C>G		intron_variant		1	NM_017935.5	P1

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83721 AN: 151636 Hom.: 24421 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.472 AC: 546313 AN: 1158374 Hom.: 129936 AF XY: 0.471 AC XY: 269638 AN XY: 573056

Gnomad4 AFR exome AF: 0.759

Gnomad4 AMR exome AF: 0.504

Gnomad4 ASJ exome AF: 0.514

Gnomad4 EAS exome AF: 0.487

Gnomad4 SAS exome AF: 0.425

Gnomad4 FIN exome AF: 0.505

Gnomad4 NFE exome AF: 0.462

Gnomad4 OTH exome AF: 0.495

GnomAD4 genome AF: 0.552 AC: 83817 AN: 151756 Hom.: 24466 Cov.: 31 AF XY: 0.557 AC XY: 41276 AN XY: 74152

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.536

Alfa AF: 0.510 Hom.: 2587

Bravo AF: 0.556

Asia WGS AF: 0.544 AC: 1889 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	0.86
DANN	Benign	0.43

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: rs10516483; hg19: chr4-102791905;