Variant chr16-1494300-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_016111.4(TELO2):c.19G>C(p.Glu7Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,612,310 control chromosomes in the GnomAD database, including 55,198 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E7G) has been classified as Benign.

Frequency

Genomes: 𝑓 0.25 ( 4970 hom., cov: 31)

Exomes 𝑓: 0.26 ( 50228 hom. )

Consequence

TELO2
NM_016111.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.895

Variant links:

Genes affected

TELO2 (HGNC:29099): (telomere maintenance 2) This gene encodes a protein that functions as an S-phase checkpoint protein in the cell cycle. The protein may also play a role in DNA repair.[provided by RefSeq, Mar 2009]

TELO2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.028985E-4).

BP6

Variant 16-1494300-G-C is Benign according to our data. Variant chr16-1494300-G-C is described in ClinVar as [Benign]. Clinvar id is 1231598.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TELO2	NM_016111.4 linkuse as main transcript	c.19G>C	p.Glu7Gln	missense_variant	2/21	ENST00000262319.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TELO2	ENST00000262319.11 linkuse as main transcript	c.19G>C	p.Glu7Gln	missense_variant	2/21	1	NM_016111.4	P1
TELO2	ENST00000497339.6 linkuse as main transcript	c.19G>C	p.Glu7Gln	missense_variant, NMD_transcript_variant	2/12	5

Frequencies

GnomAD3 genomes

AF:

0.247

AC:

37476

AN:

151696

Hom.:

4956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.220

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.519

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.251

GnomAD3 exomes

AF:

0.248

AC:

62256

AN:

250538

Hom.:

8644

AF XY:

0.248

AC XY:

33669

AN XY:

135564

show subpopulations

Gnomad AFR exome

AF:

0.219

Gnomad AMR exome

AF:

0.143

Gnomad ASJ exome

AF:

0.276

Gnomad EAS exome

AF:

0.506

Gnomad SAS exome

AF:

0.211

Gnomad FIN exome

AF:

0.237

Gnomad NFE exome

AF:

0.253

Gnomad OTH exome

AF:

0.244

GnomAD4 exome

AF:

0.255

AC:

372971

AN:

1460496

Hom.:

50228

Cov.:

AF XY:

0.255

AC XY:

184891

AN XY:

726472

show subpopulations

Gnomad4 AFR exome

AF:

0.226

Gnomad4 AMR exome

AF:

0.149

Gnomad4 ASJ exome

AF:

0.280

Gnomad4 EAS exome

AF:

0.543

Gnomad4 SAS exome

AF:

0.205

Gnomad4 FIN exome

AF:

0.241

Gnomad4 NFE exome

AF:

0.254

Gnomad4 OTH exome

AF:

0.261

GnomAD4 genome

AF:

0.247

AC:

37521

AN:

151814

Hom.:

4970

Cov.:

AF XY:

0.246

AC XY:

18238

AN XY:

74178

show subpopulations

Gnomad4 AFR

AF:

0.220

Gnomad4 AMR

AF:

0.217

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.520

Gnomad4 SAS

AF:

0.222

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.249

Hom.:

1505

Bravo

AF:

0.243

TwinsUK

AF:

0.265

AC:

984

ALSPAC

AF:

0.252

AC:

973

ESP6500AA

AF:

0.0177

AC:

ESP6500EA

AF:

0.0156

AC:

134

ExAC

AF:

0.252

AC:

30546

Asia WGS

AF:

0.388

AC:

1350

AN:

3478

EpiCase

AF:

0.259

EpiControl

AF:

0.257

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 24, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.7

DANN

Benign

0.41

DEOGEN2

Benign

0.051

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.44

LIST_S2

Benign

0.27

MetaRNN

Benign

0.00010

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.20

MutationTaster

Benign

1.0

PrimateAI

Benign

0.37

PROVEAN

Benign

-0.78

REVEL

Benign

0.066

Sift

Benign

0.53

Sift4G

Benign

0.46

Polyphen

0.0020

Vest4

0.019

MPC

0.12

ClinPred

0.0053

GERP RS

0.13

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.041

gMVP

0.13

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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