chr10-69459661-T-C

Variant names:

• chr10-69459661-T-C
• rs2894087
• NM_012339.5:c.96+7971T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012339.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN15	NM_012339.5	MANE Select	c.96+7971T>C		intron	N/A	NP_036471.1
	TSPAN15	NM_001351263.2		c.96+7971T>C		intron	N/A	NP_001338192.1
	TSPAN15	NR_147091.2		n.226+7971T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN15	ENST00000373290.7	TSL:1 MANE Select	c.96+7971T>C		intron	N/A	ENSP00000362387.2
	TSPAN15	ENST00000478112.1	TSL:2	n.214+7971T>C		intron	N/A

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

African (AFR) AF: 0.321 AC: 13288 AN: 41362

American (AMR) AF: 0.406 AC: 6195 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1680 AN: 3466

East Asian (EAS) AF: 0.164 AC: 843 AN: 5150

South Asian (SAS) AF: 0.411 AC: 1971 AN: 4800

European-Finnish (FIN) AF: 0.404 AC: 4262 AN: 10544

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30878 AN: 67930

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.414 Hom.: 1755

Bravo AF: 0.392

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.82
DANN	Benign	0.79
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2894087; hg19: chr10-71219417;