rs10030362

Variant names:

• chr4-101701686-T-C
• rs10030362
• ENST00000504592.5:c.-45-19678T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504592.5(BANK1):​c.-45-19678T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,954 control chromosomes in the GnomAD database, including 15,527 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 0.45 (15527 hom., cov: 32)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 2 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

LOC107986297 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504592.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANK1	ENST00000504592.5	TSL:2	c.-45-19678T>C		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67661 AN: 151836 Hom.: 15521 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.445 AC: 67685 AN: 151954 Hom.: 15527 Cov.: 32 AF XY: 0.435 AC XY: 32336 AN XY: 74262

African (AFR) AF: 0.434 AC: 17991 AN: 41414

American (AMR) AF: 0.365 AC: 5571 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3468

East Asian (EAS) AF: 0.193 AC: 999 AN: 5166

South Asian (SAS) AF: 0.371 AC: 1789 AN: 4826

European-Finnish (FIN) AF: 0.430 AC: 4538 AN: 10552

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33923 AN: 67960

Other (OTH) AF: 0.447 AC: 944 AN: 2114

Alfa AF: 0.459 Hom.: 3241

Bravo AF: 0.443

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.49
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10030362; hg19: chr4-102622843;