rs2631268

chr4-102027573-G-T

Variant summary

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

The NM_017935.5(BANK1):c.1594+2064G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 150,640 control chromosomes in the GnomAD database, including 6,924 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 0.30 (6924 hom., cov: 31)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANK1	NM_017935.5	c.1594+2064G>T		intron_variant		ENST00000322953.9
BANK1	NM_001083907.3	c.1504+2064G>T		intron_variant
BANK1	NM_001127507.3	c.1195+2064G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000322953.9	c.1594+2064G>T		intron_variant		1	NM_017935.5	P1
	ENST00000505091.1	n.396+4636C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45137 AN: 150524 Hom.: 6906 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.300 AC: 45185 AN: 150640 Hom.: 6924 Cov.: 31 AF XY: 0.303 AC XY: 22269 AN XY: 73496

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.326

Alfa AF: 0.286 Hom.: 12863

Bravo AF: 0.312

Asia WGS AF: 0.362 AC: 1257 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	4.8
Dann	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs2631268; hg19: chr4-102948730;