Genetic Variant ENSG00000279086:n.1104A>G (chr7-116210408-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000624389.1(ENSG00000279086):n.1104A>G 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 0.581 in 245,372 control chromosomes in the GnomAD database, including 42,441 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 ( 25061 hom., cov: 35)

Exomes 𝑓: 0.60 ( 17380 hom. )

Consequence

ENSG00000279086
ENST00000624389.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

Publications

6 publications found

Variant links:

COSMIC-nc: COSV64043800

Genes affected

ENSG00000279086 (HGNC:):

ENSG00000279086 links:

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:

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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=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TES	NM_015641.4 link	c.-300T>C		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.-300T>C		upstream_gene_variant		1	NM_015641.4	ENSP00000350937.4		Q9UGI8-1

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86384

AN:

151968

Hom.:

25010

Cov.:

show subpopulations

Gnomad AFR

AF:

0.495

Gnomad AMI

AF:

0.578

Gnomad AMR

AF:

0.635

Gnomad ASJ

AF:

0.521

Gnomad EAS

AF:

0.856

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.541

GnomAD4 exome

AF:

0.601

AC:

56047

AN:

93294

Hom.:

17380

Cov.:

AF XY:

0.600

AC XY:

28505

AN XY:

47500

show subpopulations

African (AFR)

AF:

0.497

AC:

1382

AN:

2780

American (AMR)

AF:

0.675

AC:

1646

AN:

2438

Ashkenazi Jewish (ASJ)

AF:

0.510

AC:

1731

AN:

3394

East Asian (EAS)

AF:

0.879

AC:

7298

AN:

8300

South Asian (SAS)

AF:

0.568

AC:

487

AN:

858

European-Finnish (FIN)

AF:

0.581

AC:

5193

AN:

8936

Middle Eastern (MID)

AF:

0.573

AC:

307

AN:

536

European-Non Finnish (NFE)

AF:

0.574

AC:

34464

AN:

60052

Other (OTH)

AF:

0.590

AC:

3539

AN:

6000

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1038

2076

3114

4152

5190

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.569

AC:

86487

AN:

152078

Hom.:

25061

Cov.:

AF XY:

0.575

AC XY:

42757

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.495

AC:

20562

AN:

41516

American (AMR)

AF:

0.636

AC:

9721

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.521

AC:

1808

AN:

3468

East Asian (EAS)

AF:

0.856

AC:

4414

AN:

5156

South Asian (SAS)

AF:

0.597

AC:

2887

AN:

4834

European-Finnish (FIN)

AF:

0.590

AC:

6232

AN:

10566

Middle Eastern (MID)

AF:

0.565

AC:

165

AN:

292

European-Non Finnish (NFE)

AF:

0.574

AC:

39023

AN:

67940

Other (OTH)

AF:

0.545

AC:

1151

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1998

3996

5995

7993

9991

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.573

Hom.:

3110

Bravo

AF:

0.568

Asia WGS

AF:

0.710

AC:

2464

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

0.12

PromoterAI

0.16

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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7-116210408-T-C

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