rs200043598

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001394998.1(TANC2):​c.127C>A​(p.Arg43Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000699 in 1,429,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R43C) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )

Consequence

TANC2
NM_001394998.1 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.98
Variant links:
Genes affected
TANC2 (HGNC:30212): (tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2) Predicted to be involved in dense core granule cytoskeletal transport; regulation of dendritic spine development; and regulation of dendritic spine morphogenesis. Predicted to act upstream of or within in utero embryonic development. Located in dendritic spine. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.17080972).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TANC2NM_001394998.1 linkc.127C>A p.Arg43Ser missense_variant Exon 3 of 28 ENST00000689528.1 NP_001381927.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TANC2ENST00000689528.1 linkc.127C>A p.Arg43Ser missense_variant Exon 3 of 28 NM_001394998.1 ENSP00000510600.1 A0A8I5KXR5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.99e-7
AC:
1
AN:
1429766
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
708046
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.13e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.017
T
BayesDel_noAF
Benign
-0.26
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.055
T;.;.
Eigen
Benign
-0.11
Eigen_PC
Benign
0.11
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Uncertain
0.94
D;D;D
M_CAP
Benign
0.0046
T
MetaRNN
Benign
0.17
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.0
N;N;.
PrimateAI
Uncertain
0.67
T
PROVEAN
Benign
-0.28
N;N;.
REVEL
Benign
0.14
Sift
Uncertain
0.0060
D;D;.
Sift4G
Benign
0.21
T;T;T
Polyphen
0.011
B;.;.
Vest4
0.72
MutPred
0.23
Gain of phosphorylation at R43 (P = 0.0024);Gain of phosphorylation at R43 (P = 0.0024);.;
MVP
0.50
MPC
0.32
ClinPred
0.70
D
GERP RS
5.0
Varity_R
0.19
gMVP
0.18

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-61151363; API