Variant 1-117623763-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_017709.4(TENT5C):c.895G>A(p.Glu299Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00891 in 1,614,198 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.0060 ( 3 hom., cov: 31)

Exomes 𝑓: 0.0092 ( 69 hom. )

Consequence

TENT5C
NM_017709.4 missense

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 5.38

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 -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0057156086).

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENT5C	NM_017709.4 linkuse as main transcript	c.895G>A	p.Glu299Lys	missense_variant	2/2	ENST00000369448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENT5C	ENST00000369448.4 linkuse as main transcript	c.895G>A	p.Glu299Lys	missense_variant	2/2	1	NM_017709.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00599

AC:

911

AN:

152192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00152

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00404

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00650

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.00717

GnomAD3 exomes

AF:

0.00654

AC:

1643

AN:

251366

Hom.:

AF XY:

0.00632

AC XY:

858

AN XY:

135848

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00466

Gnomad ASJ exome

AF:

0.00337

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00189

Gnomad FIN exome

AF:

0.00601

Gnomad NFE exome

AF:

0.0104

Gnomad OTH exome

AF:

0.00912

GnomAD4 exome

AF:

0.00921

AC:

13468

AN:

1461888

Hom.:

Cov.:

AF XY:

0.00909

AC XY:

6612

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00152

Gnomad4 AMR exome

AF:

0.00440

Gnomad4 ASJ exome

AF:

0.00436

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00209

Gnomad4 FIN exome

AF:

0.00717

Gnomad4 NFE exome

AF:

0.0109

Gnomad4 OTH exome

AF:

0.00712

GnomAD4 genome

AF:

0.00598

AC:

911

AN:

152310

Hom.:

Cov.:

AF XY:

0.00553

AC XY:

412

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.00152

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.00404

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00650

Gnomad4 NFE

AF:

0.0102

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00989

Hom.:

Bravo

AF:

0.00599

TwinsUK

AF:

0.0111

AC:

ALSPAC

AF:

0.0122

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.0106

AC:

ExAC

AF:

0.00663

AC:

805

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.0112

EpiControl

AF:

0.00877

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

0.18

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.45

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.20

Eigen

Uncertain

0.28

Eigen_PC

Uncertain

0.40

FATHMM_MKL

Uncertain

0.93

LIST_S2

Pathogenic

0.98

MetaRNN

Benign

0.0057

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.68

PROVEAN

Benign

-2.0

REVEL

Benign

0.11

Sift

Benign

0.21

Sift4G

Benign

0.26

Polyphen

0.16

Vest4

0.49

MVP

0.21

MPC

0.88

ClinPred

0.026

GERP RS

5.7

Varity_R

0.41

gMVP

0.82

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