10-69507167-T-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_012339.5(TSPAN15):​c.*189T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000784 in 1,275,466 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 7.8e-7 (0 hom.)
• Consequence: TSPAN15 NM_012339.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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.*189T>C		3_prime_UTR	Exon 8 of 8	NP_036471.1
	TSPAN15	NR_147091.2		n.1275T>C		non_coding_transcript_exon	Exon 8 of 8
	TSPAN15	NM_001351263.2		c.*189T>C		3_prime_UTR	Exon 6 of 6	NP_001338192.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSPAN15	ENST00000373290.7	TSL:1 MANE Select	c.*189T>C		3_prime_UTR	Exon 8 of 8	ENSP00000362387.2
	TSPAN15	ENST00000470508.1	TSL:2	n.612T>C		non_coding_transcript_exon	Exon 2 of 2
	TSPAN15	ENST00000452130.1	TSL:5	c.463-387T>C		intron	N/A	ENSP00000404528.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.84e-7 AC: 1 AN: 1275466 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 618506

African (AFR) AF: 0.00 AC: 0 AN: 27856

American (AMR) AF: 0.00 AC: 0 AN: 17818

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18658

East Asian (EAS) AF: 0.00 AC: 0 AN: 33598

South Asian (SAS) AF: 0.00 AC: 0 AN: 60624

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30794

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3580

European-Non Finnish (NFE) AF: 9.71e-7 AC: 1 AN: 1029674

Other (OTH) AF: 0.00 AC: 0 AN: 52864

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		-0.26

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;