chr4-101804916-A-G

Position:

• chr4-101804916-A-G

Variant summary

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

The NM_017935.5(BANK1):​c.70+13966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,186 control chromosomes in the GnomAD database, including 61,822 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 0.90 (61822 hom., cov: 31)
• Consequence: BANK1 NM_017935.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BANK1	NM_017935.5	c.70+13966A>G		intron_variant		ENST00000322953.9	NP_060405.5
BANK1	NM_001127507.3	c.70+13966A>G		intron_variant			NP_001120979.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BANK1	ENST00000322953.9	c.70+13966A>G		intron_variant		1	NM_017935.5	ENSP00000320509.4
BANK1	ENST00000508653.5	c.70+13966A>G		intron_variant		1		ENSP00000422314.1
BANK1	ENST00000504592.5	c.26-24892A>G		intron_variant		2		ENSP00000421443.1
BANK1	ENST00000428908.5	c.70+13966A>G		intron_variant		5		ENSP00000412748.1

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136700 AN: 152068 Hom.: 61775 Cov.: 31

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.899 AC: 136802 AN: 152186 Hom.: 61822 Cov.: 31 AF XY: 0.893 AC XY: 66412 AN XY: 74390

Gnomad4 AFR AF: 0.977

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.877

Alfa AF: 0.883 Hom.: 66063

Bravo AF: 0.897

Asia WGS AF: 0.838 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.38

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: rs6833249; hg19: chr4-102726073;