rs10516481

chr4-101737834-T-C

Variant summary

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

The XR_001741778.1(LOC107986297):n.194-16199T>C 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 0.0746 in 152,126 control chromosomes in the GnomAD database, including 508 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 0.075 (508 hom., cov: 32)
• Consequence: LOC107986297 XR_001741778.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986297	XR_001741778.1	n.194-16199T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANK1	ENST00000504592.5	c.25+16401T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11344 AN: 152008 Hom.: 509 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0680

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

GnomAD4 genome AF: 0.0746 AC: 11348 AN: 152126 Hom.: 508 Cov.: 32 AF XY: 0.0726 AC XY: 5403 AN XY: 74376

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0760

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.0673

Alfa AF: 0.0637 Hom.: 452

Bravo AF: 0.0738

Asia WGS AF: 0.0190 AC: 65 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.14
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516481; hg19: chr4-102658991;