chr4-101870748-C-G

Variant names:

• chr4-101870748-C-G
• rs10516483
• NM_017935.5:c.903+104C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

BANK1 Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017935.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	NM_017935.5	MANE Select	c.903+104C>G		intron	N/A	NP_060405.5
	BANK1	NM_001083907.3		c.813+104C>G		intron	N/A	NP_001077376.3
	BANK1	NM_001127507.3		c.504+104C>G		intron	N/A	NP_001120979.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000322953.9	TSL:1 MANE Select	c.903+104C>G		intron	N/A	ENSP00000320509.4
	BANK1	ENST00000508653.5	TSL:1	c.504+104C>G		intron	N/A	ENSP00000422314.1
	BANK1	ENST00000504592.5	TSL:2	c.858+104C>G		intron	N/A	ENSP00000421443.1

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

African (AFR) AF: 0.759 AC: 19314 AN: 25438

American (AMR) AF: 0.504 AC: 11436 AN: 22700

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 9313 AN: 18114

East Asian (EAS) AF: 0.487 AC: 16582 AN: 34040

South Asian (SAS) AF: 0.425 AC: 24003 AN: 56544

European-Finnish (FIN) AF: 0.505 AC: 18766 AN: 37172

Middle Eastern (MID) AF: 0.419 AC: 2059 AN: 4912

European-Non Finnish (NFE) AF: 0.462 AC: 420575 AN: 910458

Other (OTH) AF: 0.495 AC: 24265 AN: 48996

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

African (AFR) AF: 0.747 AC: 30930 AN: 41428

American (AMR) AF: 0.528 AC: 8038 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2882 AN: 5166

South Asian (SAS) AF: 0.438 AC: 2110 AN: 4814

European-Finnish (FIN) AF: 0.528 AC: 5549 AN: 10508

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31014 AN: 67832

Other (OTH) AF: 0.536 AC: 1131 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.43
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10516483; hg19: chr4-102791905;