Genetic Variant TEAD3:n.*1133T>C (chr6-35474620-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000402886.9(TEAD3):n.*1133T>C 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 0.303 in 176,370 control chromosomes in the GnomAD database, including 14,742 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 0.33 ( 14346 hom., cov: 32)

Exomes 𝑓: 0.14 ( 396 hom. )

Consequence

TEAD3
ENST00000402886.9 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.121

Publications

13 publications found

Variant links:

Genes affected

TEAD3 (HGNC:11716): (TEA domain transcription factor 3) This gene product is a member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is predominantly expressed in the placenta and is involved in the transactivation of the chorionic somatomammotropin-B gene enhancer. Translation of this protein is initiated at a non-AUG (AUA) start codon. [provided by RefSeq, Jul 2008]

TEAD3 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEAD3	NM_003214.4 link	c.*424T>C		3_prime_UTR_variant	Exon 13 of 13	ENST00000338863.13	NP_003205.2	Q99594
TEAD3	NM_001395214.1 link	c.*424T>C		3_prime_UTR_variant	Exon 13 of 13		NP_001382143.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TEAD3	ENST00000402886.9 link	n.*1133T>C	non_coding_transcript_exon_variant	Exon 11 of 11	1		ENSP00000384577.5	B5MCM0
TEAD3	ENST00000338863.13 link	c.*424T>C	3_prime_UTR_variant	Exon 13 of 13	1	NM_003214.4	ENSP00000345772.8	Q99594A0A1X7SBS4
TEAD3	ENST00000402886.9 link	n.*1133T>C	3_prime_UTR_variant	Exon 11 of 11	1		ENSP00000384577.5	B5MCM0

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49849

AN:

152014

Hom.:

14286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.769

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.331

Gnomad SAS

AF:

0.316

Gnomad FIN

AF:

0.0868

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.343

GnomAD4 exome

AF:

0.145

AC:

3506

AN:

24238

Hom.:

396

Cov.:

AF XY:

0.154

AC XY:

1962

AN XY:

12760

show subpopulations

African (AFR)

AF:

0.733

AC:

176

AN:

240

American (AMR)

AF:

0.190

AC:

603

AN:

3172

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

161

AN:

452

East Asian (EAS)

AF:

0.267

AC:

109

AN:

408

South Asian (SAS)

AF:

0.259

AC:

813

AN:

3144

European-Finnish (FIN)

AF:

0.0621

AC:

AN:

982

Middle Eastern (MID)

AF:

0.227

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0935

AC:

1354

AN:

14478

Other (OTH)

AF:

0.164

AC:

209

AN:

1274

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

128

257

385

514

642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

116

174

232

290

<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:

0.328

AC:

49961

AN:

152132

Hom.:

14346

Cov.:

AF XY:

0.327

AC XY:

24298

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.769

AC:

31912

AN:

41486

American (AMR)

AF:

0.248

AC:

3798

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

1326

AN:

3466

East Asian (EAS)

AF:

0.331

AC:

1714

AN:

5178

South Asian (SAS)

AF:

0.315

AC:

1521

AN:

4822

European-Finnish (FIN)

AF:

0.0868

AC:

920

AN:

10604

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7786

AN:

67976

Other (OTH)

AF:

0.347

AC:

731

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1123

2247

3370

4494

5617

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.201

Hom.:

14050

Bravo

AF:

0.363

Asia WGS

AF:

0.400

AC:

1389

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.2

(source)

DANN

Benign

0.43

PhyloP100

0.12

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over