rs2894087

Positions:

• chr10-69459661-T-C

Variant summary

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

The NM_012339.5(TSPAN15):​c.96+7971T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,844 control chromosomes in the GnomAD database, including 12,569 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 0.40 (12569 hom., cov: 30)
• Consequence: TSPAN15 NM_012339.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941

Genes affected

TSPAN15 (HGNC:23298): (tetraspanin 15) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. The use of alternate polyadenylation sites has been found for this gene. [provided by RefSeq, Jul 2008]

TSPAN15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSPAN15	NM_012339.5	c.96+7971T>C		intron_variant		ENST00000373290.7	NP_036471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSPAN15	ENST00000373290.7	c.96+7971T>C		intron_variant		1	NM_012339.5	ENSP00000362387.2
TSPAN15	ENST00000478112.1	n.214+7971T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60528 AN: 151724 Hom.: 12574 Cov.: 30

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.399 AC: 60537 AN: 151844 Hom.: 12569 Cov.: 30 AF XY: 0.395 AC XY: 29284 AN XY: 74188

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.390

Alfa AF: 0.419 Hom.: 1719

Bravo AF: 0.392

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.82
DANN	Benign	0.79

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: rs2894087; hg19: chr10-71219417;