rs12648641

chr4-101738593-C-A

Variant summary

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

The XR_001741778.1(LOC107986297):n.194-15440C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,100 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 33)
• Consequence: LOC107986297 XR_001741778.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

Genes affected

LOC107986297 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986297	XR_001741778.1	n.194-15440C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000504592.5	c.25+17160C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18542 AN: 151982 Hom.: 1286 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.122 AC: 18576 AN: 152100 Hom.: 1288 Cov.: 33 AF XY: 0.127 AC XY: 9443 AN XY: 74362

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.123

Alfa AF: 0.110 Hom.: 255

Bravo AF: 0.121

Asia WGS AF: 0.221 AC: 765 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.50
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12648641; hg19: chr4-102659750;