6-81752132-C-G

Variant summary

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

The NM_017633.3(TENT5A):​c.10G>C​(p.Gly4Arg) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

TENT5A
NM_017633.3 missense

Scores

2
3
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43
Variant links:
Genes affected
TENT5A (HGNC:18345): (terminal nucleotidyltransferase 5A) Enables RNA binding activity. Predicted to be involved in mRNA stabilization. Predicted to act upstream of or within response to bacterium. Implicated in lung non-small cell carcinoma; osteoarthritis; and osteogenesis imperfecta type 18. [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=0.13062915).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TENT5ANM_017633.3 linkuse as main transcriptc.10G>C p.Gly4Arg missense_variant 2/3 ENST00000320172.11 NP_060103.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TENT5AENST00000320172.11 linkuse as main transcriptc.10G>C p.Gly4Arg missense_variant 2/31 NM_017633.3 ENSP00000318298 A2Q96IP4-1
TENT5AENST00000369756.3 linkuse as main transcriptc.253G>C p.Gly85Arg missense_variant 2/31 ENSP00000358771
TENT5AENST00000369754.7 linkuse as main transcriptc.67G>C p.Gly23Arg missense_variant 2/31 ENSP00000358769 P4Q96IP4-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
41
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.50
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.0062
.;T;.
Eigen
Benign
-0.37
Eigen_PC
Benign
-0.18
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.81
T;T;T
M_CAP
Benign
0.052
D
MetaRNN
Benign
0.13
T;T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
0.52
D;D;D
PrimateAI
Uncertain
0.76
T
PROVEAN
Benign
0.010
N;N;N
REVEL
Benign
0.046
Sift
Uncertain
0.0020
D;D;D
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
0.0
B;B;.
Vest4
0.41
MutPred
0.32
.;Loss of sheet (P = 0.0357);.;
MVP
0.40
MPC
1.1
ClinPred
0.66
D
GERP RS
3.5
Varity_R
0.11
gMVP
0.25

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.

Other links and lift over

dbSNP: rs11040; hg19: chr6-82461849; API