Variant chr9-127717702-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 ENST00000373289.4(TTC16):c.356G>A(p.Arg119Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0044 in 1,613,942 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0033 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0045 ( 29 hom. )

Consequence

TTC16
ENST00000373289.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:2

Conservation

PhyloP100: 4.22

Variant links:

Genes affected

TTC16 (HGNC:26536): (tetratricopeptide repeat domain 16)

TTC16 links:

PTRH1 (HGNC:27039): (peptidyl-tRNA hydrolase 1 homolog) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

PTRH1 links:

PTRH1 (HGNC:):

PTRH1 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=0.013285339).

BS2

High Homozygotes in GnomAdExome4 at 29 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC16	NM_144965.3 linkuse as main transcript	c.356G>A	p.Arg119Gln	missense_variant	4/14	ENST00000373289.4	NP_659402.1	Q8NEE8-1B4DH05

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TTC16	ENST00000373289.4 linkuse as main transcript	c.356G>A	p.Arg119Gln	missense_variant	4/14	1	NM_144965.3	ENSP00000362386.3	Q8NEE8-1
PTRH1	ENST00000419060.5 linkuse as main transcript	c.-1320-743C>T		intron_variant		2		ENSP00000418661.1	Q86Y79
PTRH1	ENST00000429848.1 linkuse as main transcript	n.307-1128C>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00335

AC:

510

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00439

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00510

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.00387

AC:

973

AN:

251242

Hom.:

AF XY:

0.00385

AC XY:

523

AN XY:

135846

show subpopulations

Gnomad AFR exome

AF:

0.000616

Gnomad AMR exome

AF:

0.00252

Gnomad ASJ exome

AF:

0.000596

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000947

Gnomad FIN exome

AF:

0.00518

Gnomad NFE exome

AF:

0.00617

Gnomad OTH exome

AF:

0.00457

GnomAD4 exome

AF:

0.00451

AC:

6592

AN:

1461662

Hom.:

Cov.:

AF XY:

0.00437

AC XY:

3174

AN XY:

727128

show subpopulations

Gnomad4 AFR exome

AF:

0.000538

Gnomad4 AMR exome

AF:

0.00262

Gnomad4 ASJ exome

AF:

0.000765

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000893

Gnomad4 FIN exome

AF:

0.00592

Gnomad4 NFE exome

AF:

0.00520

Gnomad4 OTH exome

AF:

0.00402

GnomAD4 genome

AF:

0.00334

AC:

509

AN:

152280

Hom.:

Cov.:

AF XY:

0.00325

AC XY:

242

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00438

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00358

Gnomad4 NFE

AF:

0.00510

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00448

Hom.:

Bravo

AF:

0.00306

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00597

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00407

AC:

ExAC

AF:

0.00431

AC:

523

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00469

EpiControl

AF:

0.00433

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Premature ovarian insufficiency

Uncertain:1

Uncertain significance, no assertion criteria provided

research

Reproductive Development, Murdoch Childrens Research Institute

Jan 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.26

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.0066

Eigen

Benign

0.16

Eigen_PC

Benign

0.053

FATHMM_MKL

Benign

0.24

LIST_S2

Benign

0.85

M_CAP

Benign

0.031

MetaRNN

Benign

0.013

MetaSVM

Benign

-0.75

MutationAssessor

Uncertain

2.1

MutationTaster

Benign

1.0

D;N;D

PrimateAI

Benign

0.34

PROVEAN

Uncertain

-2.5

REVEL

Benign

0.22

Sift

Benign

0.068

Sift4G

Benign

0.081

Polyphen

1.0

Vest4

0.46

MVP

0.78

MPC

0.71

ClinPred

0.058

GERP RS

4.6

Varity_R

0.15

gMVP

0.10

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