Genetic Variant TACC3:c.*104A>T (chr4-1745117-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001441304.1(TACC3):c.*104A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 1,159,232 control chromosomes in the GnomAD database, including 351,204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.69 ( 38437 hom., cov: 33)

Exomes 𝑓: 0.78 ( 312767 hom. )

Consequence

TACC3
NM_001441304.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.255

Publications

14 publications found

Variant links:

Genes affected

TACC3 (HGNC:11524): (transforming acidic coiled-coil containing protein 3) This gene encodes a member of the transforming acidic colied-coil protein family. The encoded protein is a motor spindle protein that may play a role in stabilization of the mitotic spindle. This protein may also play a role in growth a differentiation of certain cancer cells. [provided by RefSeq, Nov 2011]

TACC3 links:

Genome browser will be placed here

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001441304.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TACC3	NM_006342.3	MANE Select	c.*104A>T	3_prime_UTR	Exon 16 of 16	NP_006333.1
TACC3	NM_001441304.1		c.*104A>T	3_prime_UTR	Exon 16 of 16	NP_001428233.1
TACC3	NM_001441305.1		c.*104A>T	3_prime_UTR	Exon 16 of 16	NP_001428234.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TACC3	ENST00000313288.9	TSL:1 MANE Select	c.*104A>T	3_prime_UTR	Exon 16 of 16	ENSP00000326550.4
TACC3	ENST00000918516.1		c.*104A>T	3_prime_UTR	Exon 16 of 16	ENSP00000588575.1
TACC3	ENST00000918514.1		c.*104A>T	3_prime_UTR	Exon 16 of 16	ENSP00000588573.1

Frequencies

GnomAD3 genomes

AF:

0.694

AC:

105526

AN:

151954

Hom.:

38399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.460

Gnomad AMI

AF:

0.813

Gnomad AMR

AF:

0.690

Gnomad ASJ

AF:

0.763

Gnomad EAS

AF:

0.858

Gnomad SAS

AF:

0.781

Gnomad FIN

AF:

0.771

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.802

Gnomad OTH

AF:

0.703

GnomAD4 exome

AF:

0.785

AC:

790549

AN:

1007160

Hom.:

312767

Cov.:

AF XY:

0.786

AC XY:

396192

AN XY:

504160

show subpopulations

African (AFR)

AF:

0.437

AC:

10116

AN:

23146

American (AMR)

AF:

0.675

AC:

15765

AN:

23346

Ashkenazi Jewish (ASJ)

AF:

0.760

AC:

15133

AN:

19908

East Asian (EAS)

AF:

0.847

AC:

28317

AN:

33426

South Asian (SAS)

AF:

0.778

AC:

49881

AN:

64126

European-Finnish (FIN)

AF:

0.781

AC:

30728

AN:

39366

Middle Eastern (MID)

AF:

0.737

AC:

3543

AN:

4808

European-Non Finnish (NFE)

AF:

0.799

AC:

603093

AN:

754660

Other (OTH)

AF:

0.766

AC:

33973

AN:

44374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

8086

16172

24258

32344

40430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12772

25544

38316

51088

63860

<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:

0.694

AC:

105610

AN:

152072

Hom.:

38437

Cov.:

AF XY:

0.694

AC XY:

51609

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.460

AC:

19079

AN:

41460

American (AMR)

AF:

0.690

AC:

10551

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.763

AC:

2649

AN:

3472

East Asian (EAS)

AF:

0.858

AC:

4428

AN:

5158

South Asian (SAS)

AF:

0.782

AC:

3772

AN:

4824

European-Finnish (FIN)

AF:

0.771

AC:

8149

AN:

10572

Middle Eastern (MID)

AF:

0.687

AC:

202

AN:

294

European-Non Finnish (NFE)

AF:

0.802

AC:

54545

AN:

67980

Other (OTH)

AF:

0.707

AC:

1494

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

1413

2826

4240

5653

7066

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

816

1632

2448

3264

4080

<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:

0.742

Hom.:

5314

Bravo

AF:

0.677

Asia WGS

AF:

0.806

AC:

2803

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.79

(source)

DANN

Benign

0.52

PhyloP100

-0.26

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

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