rs1864590

chr10-69496155-T-G

Variant summary

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

The NM_012339.5(TSPAN15):c.453+466T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 151,854 control chromosomes in the GnomAD database, including 1,122 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 (1122 hom., cov: 31)
• Consequence: TSPAN15 NM_012339.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSPAN15	NM_012339.5	c.453+466T>G		intron_variant		ENST00000373290.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSPAN15	ENST00000373290.7	c.453+466T>G		intron_variant		1	NM_012339.5	P1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17885 AN: 151738 Hom.: 1121 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.118 AC: 17910 AN: 151854 Hom.: 1122 Cov.: 31 AF XY: 0.118 AC XY: 8735 AN XY: 74218

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0497

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.119

Alfa AF: 0.120 Hom.: 569

Bravo AF: 0.120

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.0
Dann	Benign	0.45

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: rs1864590; hg19: chr10-71255911;