10-69507167-T-G

Variant names:

• chr10-69507167-T-G
• rs11068
• NM_012339.5:c.*189T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.81).
• 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 rank	MANE	Protein	UniProt
TSPAN15	NM_012339.5	c.*189T>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000373290.7	NP_036471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPAN15	ENST00000373290.7	c.*189T>G		3_prime_UTR_variant	Exon 8 of 8	1	NM_012339.5	ENSP00000362387.2

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

African (AFR) AF: 0.0343 AC: 954 AN: 27854

American (AMR) AF: 0.0817 AC: 1454 AN: 17804

Ashkenazi Jewish (ASJ) AF: 0.0642 AC: 1198 AN: 18654

East Asian (EAS) AF: 0.0506 AC: 1700 AN: 33592

South Asian (SAS) AF: 0.128 AC: 7781 AN: 60608

European-Finnish (FIN) AF: 0.0590 AC: 1817 AN: 30792

Middle Eastern (MID) AF: 0.0684 AC: 245 AN: 3580

European-Non Finnish (NFE) AF: 0.0690 AC: 71001 AN: 1029620

Other (OTH) AF: 0.0682 AC: 3607 AN: 52854

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

African (AFR) AF: 0.0377 AC: 1564 AN: 41490

American (AMR) AF: 0.0808 AC: 1237 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3470

East Asian (EAS) AF: 0.0493 AC: 255 AN: 5170

South Asian (SAS) AF: 0.125 AC: 605 AN: 4826

European-Finnish (FIN) AF: 0.0501 AC: 532 AN: 10618

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0682 AC: 4637 AN: 67998

Other (OTH) AF: 0.0648 AC: 137 AN: 2114

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
PhyloP100		-0.26
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: rs11068; hg19: chr10-71266923;