Variant 7-47280330-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_022748.12(TNS3):c.4122C>T(p.Pro1374Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00231 in 1,614,142 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0024 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0023 ( 24 hom. )

Consequence

TNS3
NM_022748.12 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.69

Variant links:

Genes affected

TNS3 (HGNC:21616): (tensin 3) Predicted to enable phosphatase activity. Predicted to be involved in dephosphorylation and intracellular signal transduction. Predicted to act upstream of or within cell migration; lung alveolus development; and positive regulation of cell population proliferation. Located in cytosol and focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

TNS3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 7-47280330-G-A is Benign according to our data. Variant chr7-47280330-G-A is described in ClinVar as [Benign]. Clinvar id is 728532.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.69 with no splicing effect.

BS2

High AC in GnomAd4 at 360 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNS3	NM_022748.12 linkuse as main transcript	c.4122C>T	p.Pro1374Pro	synonymous_variant	29/31	ENST00000311160.14	NP_073585.8	Q68CZ2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNS3	ENST00000311160.14 linkuse as main transcript	c.4122C>T	p.Pro1374Pro	synonymous_variant	29/31	1	NM_022748.12	ENSP00000312143.9		Q68CZ2-1

Frequencies

GnomAD3 genomes

AF:

0.00237

AC:

361

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00157

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.00131

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00870

Gnomad FIN

AF:

0.00217

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00210

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00298

AC:

743

AN:

249538

Hom.:

AF XY:

0.00353

AC XY:

478

AN XY:

135384

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00113

Gnomad ASJ exome

AF:

0.00189

Gnomad EAS exome

AF:

0.0000556

Gnomad SAS exome

AF:

0.0106

Gnomad FIN exome

AF:

0.00241

Gnomad NFE exome

AF:

0.00238

Gnomad OTH exome

AF:

0.00346

GnomAD4 exome

AF:

0.00230

AC:

3369

AN:

1461850

Hom.:

Cov.:

AF XY:

0.00263

AC XY:

1910

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.00137

Gnomad4 AMR exome

AF:

0.00136

Gnomad4 ASJ exome

AF:

0.00149

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0111

Gnomad4 FIN exome

AF:

0.00240

Gnomad4 NFE exome

AF:

0.00170

Gnomad4 OTH exome

AF:

0.00277

GnomAD4 genome

AF:

0.00236

AC:

360

AN:

152292

Hom.:

Cov.:

AF XY:

0.00247

AC XY:

184

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.00156

Gnomad4 AMR

AF:

0.00131

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00871

Gnomad4 FIN

AF:

0.00217

Gnomad4 NFE

AF:

0.00210

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00247

Hom.:

Bravo

AF:

0.00226

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.00382

EpiControl

AF:

0.00350

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2023	TNS3: BP4, BP7, BS1, BS2 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

1.8

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over