Genetic Variant TSPAN15:c.*189T>G (chr10-69507167-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.264

Publications

6 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TSPAN15	NM_012339.5	MANE Select	c.*189T>G	3_prime_UTR	Exon 8 of 8	NP_036471.1
TSPAN15	NR_147091.2		n.1275T>G	non_coding_transcript_exon	Exon 8 of 8
TSPAN15	NM_001351263.2		c.*189T>G	3_prime_UTR	Exon 6 of 6	NP_001338192.1

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

AF:

0.0607

AC:

9234

AN:

152078

Hom.:

351

Cov.:

show subpopulations

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.:

AF XY:

0.0715

AC XY:

44237

AN XY:

618446

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

4783

9567

14350

19134

23917

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2848

5696

8544

11392

14240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0607

AC:

9234

AN:

152196

Hom.:

350

Cov.:

AF XY:

0.0613

AC XY:

4561

AN XY:

74418

show subpopulations

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:

AN:

292

European-Non Finnish (NFE)

AF:

0.0682

AC:

4637

AN:

67998

Other (OTH)

AF:

0.0648

AC:

137

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

454

908

1361

1815

2269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0206

Hom.:

Bravo

AF:

0.0598

Asia WGS

AF:

0.0850

AC:

295

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.3

(source)

DANN

Benign

0.67

PhyloP100

-0.26

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over