Genetic Variant TNRC18:c.8700+3A>C (chr7-5308872-T-G) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP6

The NM_001080495.3(TNRC18):c.8700+3A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000504 in 478,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00052 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00050 ( 0 hom. )

Consequence

TNRC18
NM_001080495.3 splice_region, intron

Scores

Splicing: ADA: 0.9896

Clinical Significance

Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: 0.572

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 was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP6

Variant 7-5308872-T-G is Benign according to our data. Variant chr7-5308872-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 1206354.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr7-5308872-T-G is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNRC18	NM_001080495.3 link	c.8700+3A>C		splice_region_variant, 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+3A>C		splice_region_variant, intron_variant	Intron 29 of 29	5	NM_001080495.3	ENSP00000395538.1		O15417-1
TNRC18	ENST00000399537.8 link	c.8700+3A>C		splice_region_variant, intron_variant	Intron 29 of 29	5		ENSP00000382452.4		H9KVB4

Frequencies

GnomAD3 genomes

AF:

0.000522

AC:

AN:

51762

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000537

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00256

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00833

Gnomad NFE

AF:

0.000371

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000279

AC:

AN:

186310

AF XY:

0.000303

show subpopulations

Gnomad AFR exome

AF:

0.0000953

Gnomad AMR exome

AF:

0.000525

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000217

Gnomad OTH exome

AF:

0.000883

GnomAD4 exome

AF:

0.000502

AC:

214

AN:

426438

Hom.:

Cov.:

AF XY:

0.000538

AC XY:

119

AN XY:

221020

show subpopulations

Gnomad4 AFR exome

AF:

0.000682

AC:

AN:

11736

Gnomad4 AMR exome

AF:

0.000915

AC:

AN:

26228

Gnomad4 ASJ exome

AF:

0.000202

AC:

AN:

9902

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

9900

Gnomad4 SAS exome

AF:

0.000942

AC:

AN:

44588

Gnomad4 FIN exome

AF:

0.00

AC:

AN:

24326

Gnomad4 NFE exome

AF:

0.000389

AC:

110

AN:

282604

Gnomad4 Remaining exome

AF:

0.00138

AC:

AN:

15978

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000521

AC:

AN:

51786

Hom.:

Cov.:

AF XY:

0.000646

AC XY:

AN XY:

24778

show subpopulations

Gnomad4 AFR

AF:

0.000536

AC:

0.000535906

AN:

0.000535906

Gnomad4 AMR

AF:

0.00138

AC:

0.00137514

AN:

0.00137514

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00256

AC:

0.00255754

AN:

0.00255754

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.000371

AC:

0.000371443

AN:

0.000371443

Gnomad4 OTH

AF:

0.00

AC:

AN:

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000203

Hom.:

Bravo

AF:

0.000151

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not provided

Benign:2

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Benign

0.91

Mutation Taster

=42/58

disease causing

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

0.99

dbscSNV1_RF

Pathogenic

0.82

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