rs12649238

Variant names:

• chr4-102052830-A-C
• rs12649238
• NM_017935.5:c.1970-7381A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-102052830-A-C
• chr4-102052830-A-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.1970-7381A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,114 control chromosomes in the GnomAD database, including 4,379 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 0.23 (4379 hom., cov: 32)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.970
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANK1	NM_017935.5	c.1970-7381A>C		intron_variant	Intron 11 of 16	ENST00000322953.9	NP_060405.5
BANK1	NM_001083907.3	c.1880-7381A>C		intron_variant	Intron 11 of 16		NP_001077376.3
BANK1	NM_001127507.3	c.1571-7381A>C		intron_variant	Intron 10 of 15		NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.1970-7381A>C		intron_variant	Intron 11 of 16	1	NM_017935.5	ENSP00000320509.4

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34668 AN: 151996 Hom.: 4368 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.228 AC: 34721 AN: 152114 Hom.: 4379 Cov.: 32 AF XY: 0.231 AC XY: 17205 AN XY: 74364

African (AFR) AF: 0.278 AC: 11527 AN: 41488

American (AMR) AF: 0.307 AC: 4691 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1921 AN: 5162

South Asian (SAS) AF: 0.178 AC: 862 AN: 4830

European-Finnish (FIN) AF: 0.162 AC: 1717 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12356 AN: 67976

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.153 Hom.: 727

Bravo AF: 0.245

Asia WGS AF: 0.315 AC: 1095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.66
PhyloP100		0.97
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: rs12649238; hg19: chr4-102973987;