Variant rs1630312 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_017709.4(TENT5C):c.201C>G(p.His67Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 1,614,004 control chromosomes in the GnomAD database, including 5,006 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.11 ( 1298 hom., cov: 32)

Exomes 𝑓: 0.064 ( 3708 hom. )

Consequence

TENT5C
NM_017709.4 missense

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 0.434

Variant links:

Genes affected

TENT5C (HGNC:24712): (terminal nucleotidyltransferase 5C) Enables RNA adenylyltransferase activity. Involved in mRNA stabilization. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TENT5C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017356277).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENT5C	NM_017709.4 linkuse as main transcript	c.201C>G	p.His67Gln	missense_variant	2/2	ENST00000369448.4	NP_060179.2	Q5VWP2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENT5C	ENST00000369448.4 linkuse as main transcript	c.201C>G	p.His67Gln	missense_variant	2/2	1	NM_017709.4	ENSP00000358458.3		Q5VWP2

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16591

AN:

152006

Hom.:

1297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.0956

Gnomad AMR

AF:

0.0821

Gnomad ASJ

AF:

0.0873

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.0634

Gnomad FIN

AF:

0.0676

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0593

Gnomad OTH

AF:

0.116

GnomAD3 exomes

AF:

0.0774

AC:

19448

AN:

251420

Hom.:

977

AF XY:

0.0750

AC XY:

10188

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.223

Gnomad AMR exome

AF:

0.0691

Gnomad ASJ exome

AF:

0.0841

Gnomad EAS exome

AF:

0.119

Gnomad SAS exome

AF:

0.0661

Gnomad FIN exome

AF:

0.0630

Gnomad NFE exome

AF:

0.0575

Gnomad OTH exome

AF:

0.0771

GnomAD4 exome

AF:

0.0639

AC:

93405

AN:

1461880

Hom.:

3708

Cov.:

AF XY:

0.0635

AC XY:

46170

AN XY:

727238

show subpopulations

Gnomad4 AFR exome

AF:

0.222

Gnomad4 AMR exome

AF:

0.0730

Gnomad4 ASJ exome

AF:

0.0805

Gnomad4 EAS exome

AF:

0.0884

Gnomad4 SAS exome

AF:

0.0686

Gnomad4 FIN exome

AF:

0.0616

Gnomad4 NFE exome

AF:

0.0561

Gnomad4 OTH exome

AF:

0.0806

GnomAD4 genome

AF:

0.109

AC:

16618

AN:

152124

Hom.:

1298

Cov.:

AF XY:

0.109

AC XY:

8118

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.219

Gnomad4 AMR

AF:

0.0819

Gnomad4 ASJ

AF:

0.0873

Gnomad4 EAS

AF:

0.110

Gnomad4 SAS

AF:

0.0633

Gnomad4 FIN

AF:

0.0676

Gnomad4 NFE

AF:

0.0593

Gnomad4 OTH

AF:

0.115

Alfa

AF:

0.0246

Hom.:

1458

TwinsUK

AF:

0.0566

AC:

210

ALSPAC

AF:

0.0527

AC:

203

ExAC

AF:

0.0790

AC:

9598

EpiCase

AF:

0.0642

EpiControl

AF:

0.0663

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not specified

Other:1

not provided, no classification provided

reference population

ITMI

Sep 19, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.085

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.032

Eigen

Benign

-0.38

Eigen_PC

Benign

-0.16

FATHMM_MKL

Benign

0.32

LIST_S2

Benign

0.47

MetaRNN

Benign

0.0017

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.38

PROVEAN

Benign

-0.020

REVEL

Benign

0.087

Sift

Benign

0.18

Sift4G

Benign

0.12

Polyphen

0.0

Vest4

0.024

MutPred

0.14

Loss of methylation at R70 (P = 0.0447);

MPC

0.58

ClinPred

0.020

GERP RS

5.8

Varity_R

0.21

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over