Genetic Variant TACC2:n.3033C>A (chr10-122254089-C-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000368997.7(TACC2):n.3033C>A 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 0.252 in 1,592,272 control chromosomes in the GnomAD database, including 51,511 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 0.26 ( 5021 hom., cov: 33)

Exomes 𝑓: 0.25 ( 46490 hom. )

Consequence

TACC2
ENST00000368997.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.535

Publications

30 publications found

Variant links:

Genes affected

TACC2 (HGNC:11523): (transforming acidic coiled-coil containing protein 2) Transforming acidic coiled-coil proteins are a conserved family of centrosome- and microtubule-interacting proteins that are implicated in cancer. This gene encodes a protein that concentrates at centrosomes throughout the cell cycle. This gene lies within a chromosomal region associated with tumorigenesis. Expression of this gene is induced by erythropoietin and is thought to affect the progression of breast tumors. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

TACC2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC2	NM_206862.4 link	c.*33C>A		3_prime_UTR_variant	Exon 23 of 23	ENST00000369005.6	NP_996744.4	O95359-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACC2	ENST00000369005.6 link	c.*33C>A		3_prime_UTR_variant	Exon 23 of 23	1	NM_206862.4	ENSP00000358001.1		O95359-4

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38799

AN:

152080

Hom.:

5010

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.237

Gnomad AMR

AF:

0.278

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.272

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.244

GnomAD2 exomes

AF:

0.270

AC:

67861

AN:

251254

AF XY:

0.273

show subpopulations

Gnomad AFR exome

AF:

0.250

Gnomad AMR exome

AF:

0.290

Gnomad ASJ exome

AF:

0.273

Gnomad EAS exome

AF:

0.261

Gnomad FIN exome

AF:

0.290

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.271

GnomAD4 exome

AF:

0.252

AC:

363047

AN:

1440074

Hom.:

46490

Cov.:

AF XY:

0.255

AC XY:

182793

AN XY:

717872

show subpopulations

African (AFR)

AF:

0.242

AC:

8001

AN:

33032

American (AMR)

AF:

0.290

AC:

12952

AN:

44676

Ashkenazi Jewish (ASJ)

AF:

0.271

AC:

7042

AN:

26020

East Asian (EAS)

AF:

0.270

AC:

10708

AN:

39590

South Asian (SAS)

AF:

0.340

AC:

29140

AN:

85756

European-Finnish (FIN)

AF:

0.291

AC:

15559

AN:

53388

Middle Eastern (MID)

AF:

0.266

AC:

1527

AN:

5742

European-Non Finnish (NFE)

AF:

0.241

AC:

262905

AN:

1092146

Other (OTH)

AF:

0.255

AC:

15213

AN:

59724

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

13811

27622

41434

55245

69056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9030

18060

27090

36120

45150

<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:

0.255

AC:

38856

AN:

152198

Hom.:

5021

Cov.:

AF XY:

0.261

AC XY:

19406

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.246

AC:

10203

AN:

41512

American (AMR)

AF:

0.278

AC:

4250

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

957

AN:

3468

East Asian (EAS)

AF:

0.272

AC:

1410

AN:

5184

South Asian (SAS)

AF:

0.336

AC:

1619

AN:

4824

European-Finnish (FIN)

AF:

0.289

AC:

3061

AN:

10588

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.243

AC:

16527

AN:

68018

Other (OTH)

AF:

0.251

AC:

531

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1554

3107

4661

6214

7768

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.246

Hom.:

15204

Bravo

AF:

0.249

Asia WGS

AF:

0.323

AC:

1125

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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