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

Variant summary

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

The NM_006342.3(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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

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

Exomes 𝑓: 0.78 ( 312767 hom. )

Consequence

TACC3
NM_006342.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.255

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:

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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 (BayesDel_noAF=-0.92).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC3	NM_006342.3 link	c.*104A>T		3_prime_UTR_variant	Exon 16 of 16	ENST00000313288.9	NP_006333.1	Q9Y6A5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACC3	ENST00000313288.9 link	c.*104A>T		3_prime_UTR_variant	Exon 16 of 16	1	NM_006342.3	ENSP00000326550.4		Q9Y6A5

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

Gnomad4 AFR exome

AF:

0.437

Gnomad4 AMR exome

AF:

0.675

Gnomad4 ASJ exome

AF:

0.760

Gnomad4 EAS exome

AF:

0.847

Gnomad4 SAS exome

AF:

0.778

Gnomad4 FIN exome

AF:

0.781

Gnomad4 NFE exome

AF:

0.799

Gnomad4 OTH exome

AF:

0.766

GnomAD4 genome

AF:

0.694

AC:

105610

AN:

152072

Hom.:

38437

Cov.:

AF XY:

0.694

AC XY:

51609

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.460

Gnomad4 AMR

AF:

0.690

Gnomad4 ASJ

AF:

0.763

Gnomad4 EAS

AF:

0.858

Gnomad4 SAS

AF:

0.782

Gnomad4 FIN

AF:

0.771

Gnomad4 NFE

AF:

0.802

Gnomad4 OTH

AF:

0.707

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.79

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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