rs17031508

Variant names:

• chr4-101639133-A-C
• rs17031508
• ENST00000504592.5:c.-255-30270A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-101639133-A-C
• chr4-101639133-A-G

Variant summary

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

The ENST00000504592.5(BANK1):​c.-255-30270A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 152,234 control chromosomes in the GnomAD database, including 767 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 0.087 (767 hom., cov: 32)
• Consequence: BANK1 ENST00000504592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000504592.5	c.-255-30270A>C		intron_variant	Intron 2 of 20	2		ENSP00000421443.1

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13279 AN: 152116 Hom.: 763 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0558

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0874 AC: 13298 AN: 152234 Hom.: 767 Cov.: 32 AF XY: 0.0899 AC XY: 6689 AN XY: 74416

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0455

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.0558

Gnomad4 OTH AF: 0.0805

Alfa AF: 0.0598 Hom.: 278

Bravo AF: 0.0853

Asia WGS AF: 0.212 AC: 737 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	1.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17031508; hg19: chr4-102560290;