dbSNP rs2295879: TACC2:p.Ala2732Thr (chr10-122237461-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_206862.4(TACC2):c.8194G>A(p.Ala2732Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 1,613,346 control chromosomes in the GnomAD database, including 78,327 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.27 ( 5938 hom., cov: 32)

Exomes 𝑓: 0.31 ( 72389 hom. )

Consequence

TACC2
NM_206862.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.747

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00278607).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC2	NM_206862.4 link	c.8194G>A	p.Ala2732Thr	missense_variant	Exon 17 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.8194G>A	p.Ala2732Thr	missense_variant	Exon 17 of 23	1	NM_206862.4	ENSP00000358001.1		O95359-4

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40877

AN:

151872

Hom.:

5923

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.391

Gnomad EAS

AF:

0.253

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.314

GnomAD3 exomes

AF:

0.307

AC:

77115

AN:

251042

Hom.:

12410

AF XY:

0.314

AC XY:

42603

AN XY:

135676

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.306

Gnomad ASJ exome

AF:

0.400

Gnomad EAS exome

AF:

0.235

Gnomad SAS exome

AF:

0.395

Gnomad FIN exome

AF:

0.307

Gnomad NFE exome

AF:

0.308

Gnomad OTH exome

AF:

0.321

GnomAD4 exome

AF:

0.311

AC:

454846

AN:

1461356

Hom.:

72389

Cov.:

AF XY:

0.315

AC XY:

228710

AN XY:

726968

show subpopulations

Gnomad4 AFR exome

AF:

0.148

Gnomad4 AMR exome

AF:

0.310

Gnomad4 ASJ exome

AF:

0.401

Gnomad4 EAS exome

AF:

0.230

Gnomad4 SAS exome

AF:

0.394

Gnomad4 FIN exome

AF:

0.305

Gnomad4 NFE exome

AF:

0.310

Gnomad4 OTH exome

AF:

0.320

GnomAD4 genome

AF:

0.269

AC:

40909

AN:

151990

Hom.:

5938

Cov.:

AF XY:

0.271

AC XY:

20150

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.153

Gnomad4 AMR

AF:

0.305

Gnomad4 ASJ

AF:

0.391

Gnomad4 EAS

AF:

0.253

Gnomad4 SAS

AF:

0.381

Gnomad4 FIN

AF:

0.311

Gnomad4 NFE

AF:

0.311

Gnomad4 OTH

AF:

0.321

Alfa

AF:

0.310

Hom.:

19442

Bravo

AF:

0.260

TwinsUK

AF:

0.330

AC:

1223

ALSPAC

AF:

0.319

AC:

1228

ESP6500AA

AF:

0.159

AC:

701

ESP6500EA

AF:

0.302

AC:

2598

ExAC

AF:

0.303

AC:

36750

Asia WGS

AF:

0.351

AC:

1224

AN:

3478

EpiCase

AF:

0.312

EpiControl

AF:

0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.079

DANN

Benign

0.71

DEOGEN2

Benign

0.017

T;.;T;T;T;.;T;.;.;.;.;T;.;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.047

LIST_S2

Benign

0.53

.;.;.;T;T;T;T;T;T;T;T;T;T;T

MetaRNN

Benign

0.0028

T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

-0.34

N;.;.;.;N;.;.;.;.;.;.;.;.;.

PrimateAI

Benign

0.33

PROVEAN

Benign

0.020

N;N;N;N;N;N;N;N;N;N;N;N;N;N

REVEL

Benign

0.042

Sift

Benign

0.39

T;T;T;T;T;T;T;T;T;T;T;T;T;T

Sift4G

Benign

0.99

T;T;T;T;T;T;T;T;T;T;T;T;T;T

Polyphen

0.0

B;B;B;B;B;B;B;.;B;B;.;B;B;.

Vest4

0.019

MPC

0.095

ClinPred

0.00051

GERP RS

-6.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.019

gMVP

0.25

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over