Variant 7-5309094-G-A 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_001080495.3(TNRC18):c.8625+38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0229 in 1,557,496 control chromosomes in the GnomAD database, including 669 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.021 ( 88 hom., cov: 32)

Exomes 𝑓: 0.023 ( 581 hom. )

Consequence

TNRC18
NM_001080495.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.89

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 7-5309094-G-A is Benign according to our data. Variant chr7-5309094-G-A is described in ClinVar as [Benign]. Clinvar id is 1267338.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0622 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.8625+38C>T		intron_variant		ENST00000430969.6	NP_001073964.2	O15417-1A3KMH2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNRC18	ENST00000430969.6 linkuse as main transcript	c.8625+38C>T		intron_variant		5	NM_001080495.3	ENSP00000395538.1		O15417-1
TNRC18	ENST00000399537.8 linkuse as main transcript	c.8625+38C>T		intron_variant		5		ENSP00000382452.4		H9KVB4

Frequencies

GnomAD3 genomes

AF:

0.0214

AC:

3262

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00545

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.0654

Gnomad ASJ

AF:

0.00662

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0143

Gnomad FIN

AF:

0.0216

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0221

Gnomad OTH

AF:

0.0196

GnomAD3 exomes

AF:

0.0297

AC:

5329

AN:

179370

Hom.:

177

AF XY:

0.0269

AC XY:

2610

AN XY:

97066

show subpopulations

Gnomad AFR exome

AF:

0.00428

Gnomad AMR exome

AF:

0.101

Gnomad ASJ exome

AF:

0.00527

Gnomad EAS exome

AF:

0.0000794

Gnomad SAS exome

AF:

0.0176

Gnomad FIN exome

AF:

0.0238

Gnomad NFE exome

AF:

0.0210

Gnomad OTH exome

AF:

0.0235

GnomAD4 exome

AF:

0.0231

AC:

32440

AN:

1405226

Hom.:

581

Cov.:

AF XY:

0.0225

AC XY:

15634

AN XY:

696220

show subpopulations

Gnomad4 AFR exome

AF:

0.00373

Gnomad4 AMR exome

AF:

0.0946

Gnomad4 ASJ exome

AF:

0.00679

Gnomad4 EAS exome

AF:

0.0000542

Gnomad4 SAS exome

AF:

0.0176

Gnomad4 FIN exome

AF:

0.0219

Gnomad4 NFE exome

AF:

0.0231

Gnomad4 OTH exome

AF:

0.0179

GnomAD4 genome

AF:

0.0214

AC:

3265

AN:

152270

Hom.:

Cov.:

AF XY:

0.0224

AC XY:

1669

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00544

Gnomad4 AMR

AF:

0.0656

Gnomad4 ASJ

AF:

0.00662

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0143

Gnomad4 FIN

AF:

0.0216

Gnomad4 NFE

AF:

0.0221

Gnomad4 OTH

AF:

0.0194

Alfa

AF:

0.0201

Hom.:

Bravo

AF:

0.0249

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.047

DANN

Benign

0.50

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