dbSNP rs149654076: TENT5C:p.Ala297Thr (chr1-117623757-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The NM_017709.4(TENT5C):c.889G>A(p.Ala297Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00223 in 1,614,138 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0023 ( 5 hom. )

Consequence

TENT5C
NM_017709.4 missense

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 2.30

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=0.006619394).

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENT5C	NM_017709.4 link	c.889G>A	p.Ala297Thr	missense_variant	Exon 2 of 2	ENST00000369448.4	NP_060179.2	Q5VWP2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT5C	ENST00000369448.4 link	c.889G>A	p.Ala297Thr	missense_variant	Exon 2 of 2	1	NM_017709.4	ENSP00000358458.3		Q5VWP2

Frequencies

GnomAD3 genomes

AF:

0.00152

AC:

231

AN:

152130

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000604

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00368

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00225

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.00153

AC:

385

AN:

251318

Hom.:

AF XY:

0.00155

AC XY:

210

AN XY:

135830

show subpopulations

Gnomad AFR exome

AF:

0.000308

Gnomad AMR exome

AF:

0.000202

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.00508

Gnomad NFE exome

AF:

0.00215

Gnomad OTH exome

AF:

0.00196

GnomAD4 exome

AF:

0.00230

AC:

3366

AN:

1461890

Hom.:

Cov.:

AF XY:

0.00225

AC XY:

1634

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.000358

Gnomad4 AMR exome

AF:

0.000246

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000232

Gnomad4 FIN exome

AF:

0.00498

Gnomad4 NFE exome

AF:

0.00263

Gnomad4 OTH exome

AF:

0.00220

GnomAD4 genome

AF:

0.00152

AC:

231

AN:

152248

Hom.:

Cov.:

AF XY:

0.00148

AC XY:

110

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.000602

Gnomad4 AMR

AF:

0.000262

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00368

Gnomad4 NFE

AF:

0.00225

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00178

Hom.:

Bravo

AF:

0.00128

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00259

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00209

AC:

ExAC

AF:

0.00150

AC:

182

EpiCase

AF:

0.00153

EpiControl

AF:

0.00202

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not specified

Other:1

Sep 19, 2013

ITMI

Significance: not provided

Review Status: no classification provided

Collection Method: reference population

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.89

DEOGEN2

Benign

0.025

Eigen

Benign

-0.19

Eigen_PC

Benign

-0.034

FATHMM_MKL

Benign

0.74

LIST_S2

Uncertain

0.92

M_CAP

Benign

0.0051

MetaRNN

Benign

0.0066

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-0.52

REVEL

Benign

0.019

Sift

Benign

0.39

Sift4G

Benign

0.39

Polyphen

0.088

Vest4

0.15

MVP

0.33

MPC

0.61

ClinPred

0.0094

GERP RS

4.8

Varity_R

0.067

gMVP

0.32

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