GeneBe

rs907693838

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_206862.4(TACC2):​c.410C>G​(p.Ser137Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

TACC2
NM_206862.4 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.406

Publications

0 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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.07805711).

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

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TACC2
NM_206862.4
MANE Select
c.410C>Gp.Ser137Cys
missense
Exon 4 of 23NP_996744.4O95359-4
TACC2
NM_001438364.1
c.470C>Gp.Ser157Cys
missense
Exon 5 of 23NP_001425293.1
TACC2
NM_001291877.2
c.410C>Gp.Ser137Cys
missense
Exon 4 of 20NP_001278806.2E9PBC6

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TACC2
ENST00000369005.6
TSL:1 MANE Select
c.410C>Gp.Ser137Cys
missense
Exon 4 of 23ENSP00000358001.1O95359-4
TACC2
ENST00000515273.5
TSL:1
c.410C>Gp.Ser137Cys
missense
Exon 4 of 20ENSP00000424467.1E9PBC6
TACC2
ENST00000515603.5
TSL:1
c.410C>Gp.Ser137Cys
missense
Exon 4 of 20ENSP00000427618.1E7EMZ9

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.0000113

ClinVar

ClinVar submissions
Significance:Uncertain significance
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
6.7
DANN
Benign
0.93
DEOGEN2
Benign
0.015
T
Eigen
Benign
-0.94
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.011
N
LIST_S2
Benign
0.72
T
M_CAP
Benign
0.0070
T
MetaRNN
Benign
0.078
T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
0.34
N
PhyloP100
0.41
PrimateAI
Benign
0.42
T
PROVEAN
Benign
-0.080
N
REVEL
Benign
0.042
Sift
Uncertain
0.0070
D
Sift4G
Benign
0.085
T
Polyphen
0.80
P
Vest4
0.13
MutPred
0.19
Loss of phosphorylation at S137 (P = 0.005)
MVP
0.36
MPC
0.35
ClinPred
0.13
T
GERP RS
-0.59
Varity_R
0.049
gMVP
0.088
Mutation Taster
=99/1
polymorphism

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

Other links and lift over

dbSNP: rs907693838; hg19: chr10-123842425; API