NM_022748.12:c.3215C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_022748.12(TNS3):c.3215C>T(p.Thr1072Met) variant causes a missense change. The variant allele was found at a frequency of 0.0034 in 1,613,598 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0035 ( 63 hom. )

Consequence

TNS3
NM_022748.12 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.42

Publications

9 publications found

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 was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0038704276).

BP6

Variant 7-47303192-G-A is Benign according to our data. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-47303192-G-A is described in CliVar as Benign. Clinvar id is 716773.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0022 (335/152356) while in subpopulation SAS AF = 0.0246 (119/4828). AF 95% confidence interval is 0.0211. There are 0 homozygotes in GnomAd4. There are 199 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High AC in GnomAd4 at 335 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNS3	NM_022748.12 link	c.3215C>T	p.Thr1072Met	missense_variant	Exon 22 of 31	ENST00000311160.14	NP_073585.8	Q68CZ2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNS3	ENST00000311160.14 link	c.3215C>T	p.Thr1072Met	missense_variant	Exon 22 of 31	1	NM_022748.12	ENSP00000312143.9		Q68CZ2-1

Frequencies

GnomAD3 genomes

AF:

0.00220

AC:

335

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000434

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0246

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00219

Gnomad OTH

AF:

0.00191

GnomAD2 exomes

AF:

0.00507

AC:

1247

AN:

246168

AF XY:

0.00656

show subpopulations

Gnomad AFR exome

AF:

0.000744

Gnomad AMR exome

AF:

0.00154

Gnomad ASJ exome

AF:

0.00231

Gnomad EAS exome

AF:

0.0000557

Gnomad FIN exome

AF:

0.0000469

Gnomad NFE exome

AF:

0.00228

Gnomad OTH exome

AF:

0.00449

GnomAD4 exome

AF:

0.00353

AC:

5159

AN:

1461242

Hom.:

Cov.:

AF XY:

0.00433

AC XY:

3151

AN XY:

726950

show subpopulations

African (AFR)

AF:

0.000448

AC:

AN:

33480

American (AMR)

AF:

0.00163

AC:

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.00180

AC:

AN:

26132

East Asian (EAS)

AF:

0.000252

AC:

AN:

39700

South Asian (SAS)

AF:

0.0282

AC:

2429

AN:

86252

European-Finnish (FIN)

AF:

0.000132

AC:

AN:

52830

Middle Eastern (MID)

AF:

0.00971

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00205

AC:

2275

AN:

1111986

Other (OTH)

AF:

0.00409

AC:

247

AN:

60376

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

375

750

1124

1499

1874

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

204

306

408

510

<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:

0.00220

AC:

335

AN:

152356

Hom.:

Cov.:

AF XY:

0.00267

AC XY:

199

AN XY:

74502

show subpopulations

African (AFR)

AF:

0.000433

AC:

AN:

41592

American (AMR)

AF:

0.00242

AC:

AN:

15314

Ashkenazi Jewish (ASJ)

AF:

0.00173

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5178

South Asian (SAS)

AF:

0.0246

AC:

119

AN:

4828

European-Finnish (FIN)

AF:

0.0000941

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00219

AC:

149

AN:

68026

Other (OTH)

AF:

0.00189

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00264

Hom.:

Bravo

AF:

0.00181

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.000250

AC:

ESP6500EA

AF:

0.00217

AC:

ExAC

AF:

0.00524

AC:

634

Asia WGS

AF:

0.00693

AC:

AN:

3478

EpiCase

AF:

0.00393

EpiControl

AF:

0.00368

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 01, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.096

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Uncertain

-0.070

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.11

T;.

Eigen

Uncertain

0.29

Eigen_PC

Uncertain

0.33

FATHMM_MKL

Benign

0.60

LIST_S2

Uncertain

0.88

D;D

MetaRNN

Benign

0.0039

T;T

MetaSVM

Uncertain

0.18

MutationAssessor

Uncertain

2.4

M;.

PhyloP100

4.4

PrimateAI

Benign

0.46

PROVEAN

Benign

-1.9

N;N

REVEL

Benign

0.27

Sift

Uncertain

0.022

D;D

Sift4G

Uncertain

0.010

D;.

Polyphen

0.99

D;.

Vest4

0.21

MVP

0.67

ClinPred

0.035

GERP RS

5.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.063

gMVP

0.30

Mutation Taster

=100/0

polymorphism

(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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over