dbSNP rs28411392: TES:n.4C>T (chr7-116210509-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000461440.5(TES):n.4C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 468,394 control chromosomes in the GnomAD database, including 82,293 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 0.57 ( 25010 hom., cov: 34)

Exomes 𝑓: 0.59 ( 57283 hom. )

Consequence

TES
ENST00000461440.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.682

Publications

8 publications found

Variant links:

Genes affected

TES (HGNC:14620): (testin LIM domain protein) Cancer-associated chromosomal changes often involve regions containing fragile sites. This gene maps to a common fragile site on chromosome 7q31.2 designated FRA7G. This gene is similar to mouse Testin, a testosterone-responsive gene encoding a Sertoli cell secretory protein containing three LIM domains. LIM domains are double zinc-finger motifs that mediate protein-protein interactions between transcription factors, cytoskeletal proteins and signaling proteins. This protein is a negative regulator of cell growth and may act as a tumor suppressor. This scaffold protein may also play a role in cell adhesion, cell spreading and in the reorganization of the actin cytoskeleton. Multiple protein isoforms are encoded by transcript variants of this gene.[provided by RefSeq, Aug 2023]

TES links:

ENSG00000279086 (HGNC:):

ENSG00000279086 links:

Genome browser will be placed here

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=-0.59).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TES	NM_015641.4 link	c.-199C>T		upstream_gene_variant		ENST00000358204.9	NP_056456.1	Q9UGI8-1A4D0U5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TES	ENST00000358204.9 link	c.-199C>T		upstream_gene_variant		1	NM_015641.4	ENSP00000350937.4		Q9UGI8-1

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86255

AN:

151806

Hom.:

24959

Cov.:

show subpopulations

Gnomad AFR

AF:

0.495

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.635

Gnomad ASJ

AF:

0.521

Gnomad EAS

AF:

0.857

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.588

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.541

GnomAD4 exome

AF:

0.594

AC:

187932

AN:

316480

Hom.:

57283

Cov.:

AF XY:

0.593

AC XY:

93598

AN XY:

157890

show subpopulations

African (AFR)

AF:

0.499

AC:

3634

AN:

7288

American (AMR)

AF:

0.674

AC:

4003

AN:

5936

Ashkenazi Jewish (ASJ)

AF:

0.508

AC:

3959

AN:

7794

East Asian (EAS)

AF:

0.879

AC:

17163

AN:

19520

South Asian (SAS)

AF:

0.574

AC:

2385

AN:

4152

European-Finnish (FIN)

AF:

0.572

AC:

18088

AN:

31648

Middle Eastern (MID)

AF:

0.575

AC:

717

AN:

1248

European-Non Finnish (NFE)

AF:

0.577

AC:

128296

AN:

222494

Other (OTH)

AF:

0.591

AC:

9687

AN:

16400

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

3531

7063

10594

14126

17657

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2338

4676

7014

9352

11690

<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:

0.568

AC:

86357

AN:

151914

Hom.:

25010

Cov.:

AF XY:

0.575

AC XY:

42684

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.495

AC:

20539

AN:

41478

American (AMR)

AF:

0.636

AC:

9722

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.521

AC:

1808

AN:

3472

East Asian (EAS)

AF:

0.857

AC:

4387

AN:

5118

South Asian (SAS)

AF:

0.597

AC:

2881

AN:

4826

European-Finnish (FIN)

AF:

0.588

AC:

6188

AN:

10520

Middle Eastern (MID)

AF:

0.565

AC:

165

AN:

292

European-Non Finnish (NFE)

AF:

0.574

AC:

38990

AN:

67896

Other (OTH)

AF:

0.545

AC:

1151

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1939

3878

5816

7755

9694

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

740

1480

2220

2960

3700

<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:

0.573

Hom.:

3109

Bravo

AF:

0.568

Asia WGS

AF:

0.709

AC:

2440

AN:

3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

0.68

PromoterAI

0.18

Neutral

(source)

Mutation Taster

=300/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over