Genetic Variant TNRC18:c.8701-34dupC (chr7-5308345-T-TG) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001080495.3(TNRC18):c.8701-34dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,579,180 control chromosomes in the GnomAD database, including 18,749 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 1900 hom., cov: 31)

Exomes 𝑓: 0.13 ( 16849 hom. )

Consequence

TNRC18
NM_001080495.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.125

Publications

1 publications found

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: Benign. The variant received -10 ACMG points.

BP6

Variant 7-5308345-T-TG is Benign according to our data. Variant chr7-5308345-T-TG is described in ClinVar as Benign. ClinVar VariationId is 1281096.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080495.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNRC18	NM_001080495.3	MANE Select	c.8701-34dupC		intron	N/A	NP_001073964.2	O15417-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNRC18	ENST00000430969.6	TSL:5 MANE Select	c.8701-34_8701-33insC		intron	N/A	ENSP00000395538.1	O15417-1
	TNRC18	ENST00000399537.8	TSL:5	c.8701-34_8701-33insC		intron	N/A	ENSP00000382452.4	H9KVB4

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19785

AN:

150588

Hom.:

1902

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0981

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.0959

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.112

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.142

GnomAD2 exomes

AF:

0.102

AC:

17384

AN:

171094

AF XY:

0.0981

show subpopulations

Gnomad AFR exome

AF:

0.0594

Gnomad AMR exome

AF:

0.107

Gnomad ASJ exome

AF:

0.0430

Gnomad EAS exome

AF:

0.479

Gnomad FIN exome

AF:

0.0803

Gnomad NFE exome

AF:

0.0468

Gnomad OTH exome

AF:

0.0902

GnomAD4 exome

AF:

0.128

AC:

182790

AN:

1428470

Hom.:

16849

Cov.:

AF XY:

0.131

AC XY:

93032

AN XY:

707936

show subpopulations

African (AFR)

AF:

0.0912

AC:

2981

AN:

32676

American (AMR)

AF:

0.163

AC:

6499

AN:

39846

Ashkenazi Jewish (ASJ)

AF:

0.0970

AC:

2476

AN:

25532

East Asian (EAS)

AF:

0.527

AC:

19773

AN:

37532

South Asian (SAS)

AF:

0.280

AC:

22898

AN:

81788

European-Finnish (FIN)

AF:

0.137

AC:

6984

AN:

50886

Middle Eastern (MID)

AF:

0.112

AC:

613

AN:

5456

European-Non Finnish (NFE)

AF:

0.102

AC:

111909

AN:

1095652

Other (OTH)

AF:

0.146

AC:

8657

AN:

59102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

7295

14590

21886

29181

36476

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4434

8868

13302

17736

22170

<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:

0.131

AC:

19796

AN:

150710

Hom.:

1900

Cov.:

AF XY:

0.140

AC XY:

10329

AN XY:

73656

show subpopulations

African (AFR)

AF:

0.0982

AC:

3976

AN:

40490

American (AMR)

AF:

0.150

AC:

2277

AN:

15208

Ashkenazi Jewish (ASJ)

AF:

0.0959

AC:

331

AN:

3452

East Asian (EAS)

AF:

0.543

AC:

2777

AN:

5116

South Asian (SAS)

AF:

0.318

AC:

1516

AN:

4766

European-Finnish (FIN)

AF:

0.143

AC:

1504

AN:

10542

Middle Eastern (MID)

AF:

0.100

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.103

AC:

6990

AN:

67842

Other (OTH)

AF:

0.145

AC:

303

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

835

1670

2506

3341

4176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.0483

Hom.:

Bravo

AF:

0.126

Asia WGS

AF:

0.403

AC:

1400

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over