dbSNP rs3763763: TACC2:c.*33C>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 NM_206862.4(TACC2):c.*33C>A variant causes a 3 prime UTR 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
NM_206862.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.535

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

Gnomad4 AFR exome

AF:

0.242

AC:

8001

AN:

33032

Gnomad4 AMR exome

AF:

0.290

AC:

12952

AN:

44676

Gnomad4 ASJ exome

AF:

0.271

AC:

7042

AN:

26020

Gnomad4 EAS exome

AF:

0.270

AC:

10708

AN:

39590

Gnomad4 SAS exome

AF:

0.340

AC:

29140

AN:

85756

Gnomad4 FIN exome

AF:

0.291

AC:

15559

AN:

53388

Gnomad4 NFE exome

AF:

0.241

AC:

262905

AN:

1092146

Gnomad4 Remaining exome

AF:

0.255

AC:

15213

AN:

59724

Heterozygous variant carriers

13811

27622

41434

55245

69056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

Gnomad4 AFR

AF:

0.246

AC:

0.245784

AN:

0.245784

Gnomad4 AMR

AF:

0.278

AC:

0.278032

AN:

0.278032

Gnomad4 ASJ

AF:

0.276

AC:

0.275952

AN:

0.275952

Gnomad4 EAS

AF:

0.272

AC:

0.271991

AN:

0.271991

Gnomad4 SAS

AF:

0.336

AC:

0.335614

AN:

0.335614

Gnomad4 FIN

AF:

0.289

AC:

0.289101

AN:

0.289101

Gnomad4 NFE

AF:

0.243

AC:

0.24298

AN:

0.24298

Gnomad4 OTH

AF:

0.251

AC:

0.251183

AN:

0.251183

Heterozygous variant carriers

1554

3107

4661

6214

7768

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

DANN

Benign

0.87

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

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