Variant 7-5308851-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001080495.3(TNRC18):c.8700+24T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0063 ( 0 hom., cov: 0)

Exomes 𝑓: 0.16 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TNRC18
NM_001080495.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.768

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 Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 7-5308851-A-C is Benign according to our data. Variant chr7-5308851-A-C is described in ClinVar as [Benign]. Clinvar id is 1242552.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNRC18	NM_001080495.3 link	c.8700+24T>G		intron_variant	Intron 29 of 29	ENST00000430969.6	NP_001073964.2	O15417-1A3KMH2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNRC18	ENST00000430969.6 link	c.8700+24T>G		intron_variant	Intron 29 of 29	5	NM_001080495.3	ENSP00000395538.1		O15417-1
TNRC18	ENST00000399537.8 link	c.8700+24T>G		intron_variant	Intron 29 of 29	5		ENSP00000382452.4		H9KVB4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

219

AN:

34774

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00745

Gnomad AMI

AF:

0.00746

Gnomad AMR

AF:

0.00681

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00232

Gnomad SAS

AF:

0.00422

Gnomad FIN

AF:

0.0105

Gnomad MID

AF:

0.0114

Gnomad NFE

AF:

0.00575

Gnomad OTH

AF:

0.0158

GnomAD3 exomes

AF:

0.0139

AC:

960

AN:

68862

Hom.:

AF XY:

0.0128

AC XY:

492

AN XY:

38316

show subpopulations

Gnomad AFR exome

AF:

0.00391

Gnomad AMR exome

AF:

0.0569

Gnomad ASJ exome

AF:

0.0120

Gnomad EAS exome

AF:

0.0380

Gnomad SAS exome

AF:

0.0136

Gnomad FIN exome

AF:

0.00301

Gnomad NFE exome

AF:

0.00753

Gnomad OTH exome

AF:

0.0251

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.164

AC:

37399

AN:

228612

Hom.:

Cov.:

AF XY:

0.151

AC XY:

17575

AN XY:

116120

show subpopulations

Gnomad4 AFR exome

AF:

0.152

Gnomad4 AMR exome

AF:

0.163

Gnomad4 ASJ exome

AF:

0.0798

Gnomad4 EAS exome

AF:

0.0635

Gnomad4 SAS exome

AF:

0.0906

Gnomad4 FIN exome

AF:

0.0187

Gnomad4 NFE exome

AF:

0.194

Gnomad4 OTH exome

AF:

0.150

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00632

AC:

220

AN:

34820

Hom.:

Cov.:

AF XY:

0.00567

AC XY:

AN XY:

17464

show subpopulations

Gnomad4 AFR

AF:

0.00754

Gnomad4 AMR

AF:

0.00680

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00232

Gnomad4 SAS

AF:

0.00419

Gnomad4 FIN

AF:

0.0105

Gnomad4 NFE

AF:

0.00575

Gnomad4 OTH

AF:

0.0155

Alfa

AF:

0.00261

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.11

DANN

Benign

0.40

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