rs78149003

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_206862.4(TACC2):c.452C>T(p.Ala151Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00621 in 1,612,914 control chromosomes in the GnomAD database, including 235 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 105 hom., cov: 32)

Exomes 𝑓: 0.0046 ( 130 hom. )

Consequence

TACC2
NM_206862.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.291

Publications

7 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002523601).

BP6

Variant 10-122082952-C-T is Benign according to our data. Variant chr10-122082952-C-T is described in ClinVar as Benign. ClinVar VariationId is 784170.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206862.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TACC2	NM_206862.4	MANE Select	c.452C>T	p.Ala151Val	missense	Exon 4 of 23	NP_996744.4	O95359-4
TACC2	NM_001438364.1		c.512C>T	p.Ala171Val	missense	Exon 5 of 23	NP_001425293.1
TACC2	NM_001291877.2		c.452C>T	p.Ala151Val	missense	Exon 4 of 20	NP_001278806.2	E9PBC6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TACC2	ENST00000369005.6	TSL:1 MANE Select	c.452C>T	p.Ala151Val	missense	Exon 4 of 23	ENSP00000358001.1	O95359-4
TACC2	ENST00000515273.5	TSL:1	c.452C>T	p.Ala151Val	missense	Exon 4 of 20	ENSP00000424467.1	E9PBC6
TACC2	ENST00000515603.5	TSL:1	c.452C>T	p.Ala151Val	missense	Exon 4 of 20	ENSP00000427618.1	E7EMZ9

Frequencies

GnomAD3 genomes

AF:

0.0221

AC:

3366

AN:

152088

Hom.:

105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0636

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0270

Gnomad ASJ

AF:

0.0346

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00204

Gnomad OTH

AF:

0.0210

GnomAD2 exomes

AF:

0.0105

AC:

2618

AN:

249398

AF XY:

0.00865

show subpopulations

Gnomad AFR exome

AF:

0.0626

Gnomad AMR exome

AF:

0.0255

Gnomad ASJ exome

AF:

0.0346

Gnomad EAS exome

AF:

0.0000545

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00244

Gnomad OTH exome

AF:

0.0125

GnomAD4 exome

AF:

0.00456

AC:

6654

AN:

1460708

Hom.:

130

Cov.:

AF XY:

0.00436

AC XY:

3171

AN XY:

726656

show subpopulations

African (AFR)

AF:

0.0648

AC:

2168

AN:

33480

American (AMR)

AF:

0.0254

AC:

1134

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0336

AC:

877

AN:

26136

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39700

South Asian (SAS)

AF:

0.00122

AC:

105

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52270

Middle Eastern (MID)

AF:

0.0208

AC:

120

AN:

5768

European-Non Finnish (NFE)

AF:

0.00147

AC:

1635

AN:

1111990

Other (OTH)

AF:

0.0102

AC:

614

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

441

883

1324

1766

2207

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

240

360

480

600

<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:

0.0221

AC:

3366

AN:

152206

Hom.:

105

Cov.:

AF XY:

0.0221

AC XY:

1643

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.0635

AC:

2635

AN:

41516

American (AMR)

AF:

0.0270

AC:

413

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0346

AC:

120

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5152

South Asian (SAS)

AF:

0.00124

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00204

AC:

139

AN:

68016

Other (OTH)

AF:

0.0208

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

150

301

451

602

752

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.00922

Hom.:

Bravo

AF:

0.0262

TwinsUK

AF:

0.00189

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.0488

AC:

215

ESP6500EA

AF:

0.00233

AC:

ExAC

AF:

0.00979

AC:

1189

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.00344

EpiControl

AF:

0.00391

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.33

(source)

DANN

Benign

0.83

DEOGEN2

Benign

0.015

Eigen

Benign

-2.0

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.0053

LIST_S2

Benign

0.59

MetaRNN

Benign

0.0025

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.0

PhyloP100

-0.29

PrimateAI

Benign

0.24

PROVEAN

Benign

0.19

REVEL

Benign

0.046

Sift

Benign

1.0

Sift4G

Benign

0.17

Polyphen

0.0

Vest4

0.087

MPC

0.098

ClinPred

0.0035

GERP RS

-10

Varity_R

0.019

gMVP

0.061

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over