Variant 7-5308118-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001080495.3(TNRC18):c.8895C>T(p.Pro2965=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,551,608 control chromosomes in the GnomAD database, including 50,114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 3582 hom., cov: 33)

Exomes 𝑓: 0.25 ( 46532 hom. )

Consequence

TNRC18
NM_001080495.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.01

Variant links:

Genes affected

TNRC18 (HGNC:11962): (trinucleotide repeat containing 18) Predicted to enable chromatin binding activity. Located in cytosol; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TNRC18 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP6

Variant 7-5308118-G-A is Benign according to our data. Variant chr7-5308118-G-A is described in ClinVar as [Benign]. Clinvar id is 1241916.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNRC18	NM_001080495.3 linkuse as main transcript	c.8895C>T	p.Pro2965=	synonymous_variant	30/30	ENST00000430969.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNRC18	ENST00000430969.6 linkuse as main transcript	c.8895C>T	p.Pro2965=	synonymous_variant	30/30	5	NM_001080495.3	P4	O15417-1
TNRC18	ENST00000399537.8 linkuse as main transcript	c.8895C>T	p.Pro2965=	synonymous_variant	30/30	5		A2

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30083

AN:

152072

Hom.:

3583

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0819

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.323

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.178

GnomAD3 exomes

AF:

0.205

AC:

32712

AN:

159240

Hom.:

3953

AF XY:

0.203

AC XY:

17163

AN XY:

84540

show subpopulations

Gnomad AFR exome

AF:

0.0745

Gnomad AMR exome

AF:

0.148

Gnomad ASJ exome

AF:

0.206

Gnomad EAS exome

AF:

0.121

Gnomad SAS exome

AF:

0.103

Gnomad FIN exome

AF:

0.319

Gnomad NFE exome

AF:

0.268

Gnomad OTH exome

AF:

0.208

GnomAD4 exome

AF:

0.250

AC:

350311

AN:

1399416

Hom.:

46532

Cov.:

AF XY:

0.246

AC XY:

170024

AN XY:

690462

show subpopulations

Gnomad4 AFR exome

AF:

0.0720

Gnomad4 AMR exome

AF:

0.152

Gnomad4 ASJ exome

AF:

0.212

Gnomad4 EAS exome

AF:

0.132

Gnomad4 SAS exome

AF:

0.106

Gnomad4 FIN exome

AF:

0.315

Gnomad4 NFE exome

AF:

0.273

Gnomad4 OTH exome

AF:

0.229

GnomAD4 genome

AF:

0.198

AC:

30077

AN:

152192

Hom.:

3582

Cov.:

AF XY:

0.197

AC XY:

14674

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.0817

Gnomad4 AMR

AF:

0.174

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.126

Gnomad4 SAS

AF:

0.101

Gnomad4 FIN

AF:

0.323

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.176

Alfa

AF:

0.232

Hom.:

4222

Bravo

AF:

0.182

Asia WGS

AF:

0.102

AC:

353

AN:

3478

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

May 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

1.2

DANN

Benign

0.91

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