chr4-102049030-T-C

Variant names:

• chr4-102049030-T-C
• rs3113677
• NM_017935.5:c.1969+5123T>C

Variant summary

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

The NM_017935.5(BANK1):​c.1969+5123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 152,186 control chromosomes in the GnomAD database, including 67,451 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 0.94 (67451 hom., cov: 31)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.981 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.1969+5123T>C		intron	N/A	NP_060405.5
	BANK1	NM_001083907.3		c.1879+5123T>C		intron	N/A	NP_001077376.3
	BANK1	NM_001127507.3		c.1570+5123T>C		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.1969+5123T>C		intron	N/A	ENSP00000320509.4
	BANK1	ENST00000508653.5	TSL:1	c.1570+5123T>C		intron	N/A	ENSP00000422314.1
	BANK1	ENST00000504592.5	TSL:2	c.1924+5123T>C		intron	N/A	ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143023 AN: 152066 Hom.: 67411 Cov.: 31

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.951

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

GnomAD4 genome AF: 0.940 AC: 143113 AN: 152186 Hom.: 67451 Cov.: 31 AF XY: 0.936 AC XY: 69644 AN XY: 74376

African (AFR) AF: 0.989 AC: 41093 AN: 41554

American (AMR) AF: 0.927 AC: 14164 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3304 AN: 3468

East Asian (EAS) AF: 0.816 AC: 4212 AN: 5162

South Asian (SAS) AF: 0.842 AC: 4044 AN: 4802

European-Finnish (FIN) AF: 0.897 AC: 9500 AN: 10592

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63656 AN: 68008

Other (OTH) AF: 0.947 AC: 1998 AN: 2110

Alfa AF: 0.913 Hom.: 2946

Bravo AF: 0.947

Asia WGS AF: 0.856 AC: 2979 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.56
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: rs3113677; hg19: chr4-102970187;