10-69507167-T-G

Position:

• chr10-69507167-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.*189T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 1,427,554 control chromosomes in the GnomAD database, including 3,698 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 0.061 (350 hom., cov: 33)
  • Exomes 𝑓: 0.070 (3348 hom.)
• Consequence: TSPAN15 NM_012339.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSPAN15	NM_012339.5	c.*189T>G		3_prime_UTR_variant	8/8	ENST00000373290.7	NP_036471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSPAN15	ENST00000373290.7	c.*189T>G		3_prime_UTR_variant	8/8	1	NM_012339.5	ENSP00000362387.2
TSPAN15	ENST00000452130.1	c.463-387T>G		intron_variant		5		ENSP00000404528.1
TSPAN15	ENST00000470508.1	n.612T>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9234 AN: 152078 Hom.: 351 Cov.: 33

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.0655

GnomAD4 exome AF: 0.0704 AC: 89757 AN: 1275358 Hom.: 3348 Cov.: 30 AF XY: 0.0715 AC XY: 44237 AN XY: 618446

Gnomad4 AFR exome AF: 0.0343

Gnomad4 AMR exome AF: 0.0817

Gnomad4 ASJ exome AF: 0.0642

Gnomad4 EAS exome AF: 0.0506

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.0590

Gnomad4 NFE exome AF: 0.0690

Gnomad4 OTH exome AF: 0.0682

GnomAD4 genome AF: 0.0607 AC: 9234 AN: 152196 Hom.: 350 Cov.: 33 AF XY: 0.0613 AC XY: 4561 AN XY: 74418

Gnomad4 AFR AF: 0.0377

Gnomad4 AMR AF: 0.0808

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.0493

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0501

Gnomad4 NFE AF: 0.0682

Gnomad4 OTH AF: 0.0648

Alfa AF: 0.0206 Hom.: 16

Bravo AF: 0.0598

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.67

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: rs11068; hg19: chr10-71266923;