Variant chr7-5308115-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001080495.3(TNRC18):c.8898G>A(p.Val2966=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 1,550,894 control chromosomes in the GnomAD database, including 2,403 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.046 ( 183 hom., cov: 34)

Exomes 𝑓: 0.053 ( 2220 hom. )

Consequence

TNRC18
NM_001080495.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.06

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 7-5308115-C-T is Benign according to our data. Variant chr7-5308115-C-T is described in ClinVar as [Benign]. Clinvar id is 1275015.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNRC18	NM_001080495.3 linkuse as main transcript	c.8898G>A	p.Val2966=	synonymous_variant	30/30	ENST00000430969.6	NP_001073964.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNRC18	ENST00000430969.6 linkuse as main transcript	c.8898G>A	p.Val2966=	synonymous_variant	30/30	5	NM_001080495.3	ENSP00000395538	P4	O15417-1
TNRC18	ENST00000399537.8 linkuse as main transcript	c.8898G>A	p.Val2966=	synonymous_variant	30/30	5		ENSP00000382452	A2

Frequencies

GnomAD3 genomes

AF:

0.0456

AC:

6936

AN:

152148

Hom.:

183

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0270

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0482

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.0201

Gnomad SAS

AF:

0.0426

Gnomad FIN

AF:

0.0247

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0572

Gnomad OTH

AF:

0.0503

GnomAD3 exomes

AF:

0.0497

AC:

7851

AN:

158052

Hom.:

269

AF XY:

0.0502

AC XY:

4209

AN XY:

83886

show subpopulations

Gnomad AFR exome

AF:

0.0292

Gnomad AMR exome

AF:

0.0389

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.0183

Gnomad SAS exome

AF:

0.0409

Gnomad FIN exome

AF:

0.0290

Gnomad NFE exome

AF:

0.0578

Gnomad OTH exome

AF:

0.0567

GnomAD4 exome

AF:

0.0531

AC:

74234

AN:

1398628

Hom.:

2220

Cov.:

AF XY:

0.0529

AC XY:

36478

AN XY:

690046

show subpopulations

Gnomad4 AFR exome

AF:

0.0270

Gnomad4 AMR exome

AF:

0.0373

Gnomad4 ASJ exome

AF:

0.141

Gnomad4 EAS exome

AF:

0.0267

Gnomad4 SAS exome

AF:

0.0421

Gnomad4 FIN exome

AF:

0.0297

Gnomad4 NFE exome

AF:

0.0548

Gnomad4 OTH exome

AF:

0.0559

GnomAD4 genome

AF:

0.0456

AC:

6939

AN:

152266

Hom.:

183

Cov.:

AF XY:

0.0440

AC XY:

3276

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0270

Gnomad4 AMR

AF:

0.0483

Gnomad4 ASJ

AF:

0.140

Gnomad4 EAS

AF:

0.0202

Gnomad4 SAS

AF:

0.0427

Gnomad4 FIN

AF:

0.0247

Gnomad4 NFE

AF:

0.0572

Gnomad4 OTH

AF:

0.0498

Alfa

AF:

0.0500

Hom.:

122

Bravo

AF:

0.0468

Asia WGS

AF:

0.0330

AC:

113

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

-0.40

CADD

Benign

7.1

DANN

Benign

0.89

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