Genetic Variant NM_007110.5:c.1929-147C>T (chr14-20391914-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007110.5(TEP1):c.1929-147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 777,976 control chromosomes in the GnomAD database, including 102,256 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 25330 hom., cov: 30)

Exomes 𝑓: 0.49 ( 76926 hom. )

Consequence

TEP1
NM_007110.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47

Publications

13 publications found

Variant links:

Genes affected

TEP1 (HGNC:11726): (telomerase associated protein 1) This gene product is a component of the ribonucleoprotein complex responsible for telomerase activity which catalyzes the addition of new telomeres on the chromosome ends. The telomerase-associated proteins are conserved from ciliates to humans. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

TEP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEP1	NM_007110.5 link	c.1929-147C>T		intron_variant	Intron 12 of 54	ENST00000262715.10	NP_009041.2	Q99973-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TEP1	ENST00000262715.10 link	c.1929-147C>T	intron_variant	Intron 12 of 54	1	NM_007110.5	ENSP00000262715.5	Q99973-1
TEP1	ENST00000556935.5 link	c.1605-147C>T	intron_variant	Intron 10 of 52	1		ENSP00000452574.1	G3V5X7
TEP1	ENST00000555727.5 link	n.1929-147C>T	intron_variant	Intron 12 of 53	1		ENSP00000451634.1	G3V470
TEP1	ENST00000555008.5 link	n.-169C>T	upstream_gene_variant		1		ENSP00000450541.1	G3V2A4

Frequencies

GnomAD3 genomes

AF:

0.565

AC:

85666

AN:

151618

Hom.:

25277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.739

Gnomad AMI

AF:

0.458

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.487

Gnomad EAS

AF:

0.617

Gnomad SAS

AF:

0.553

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.544

GnomAD4 exome

AF:

0.488

AC:

305432

AN:

626240

Hom.:

76926

AF XY:

0.489

AC XY:

157719

AN XY:

322656

show subpopulations

African (AFR)

AF:

0.742

AC:

11676

AN:

15734

American (AMR)

AF:

0.614

AC:

12643

AN:

20576

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

7171

AN:

14958

East Asian (EAS)

AF:

0.571

AC:

18200

AN:

31874

South Asian (SAS)

AF:

0.547

AC:

27857

AN:

50924

European-Finnish (FIN)

AF:

0.428

AC:

14132

AN:

33002

Middle Eastern (MID)

AF:

0.453

AC:

1262

AN:

2784

European-Non Finnish (NFE)

AF:

0.463

AC:

196661

AN:

424728

Other (OTH)

AF:

0.500

AC:

15830

AN:

31660

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

7313

14627

21940

29254

36567

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3524

7048

10572

14096

17620

<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:

0.565

AC:

85775

AN:

151736

Hom.:

25330

Cov.:

AF XY:

0.563

AC XY:

41713

AN XY:

74108

show subpopulations

African (AFR)

AF:

0.739

AC:

30600

AN:

41382

American (AMR)

AF:

0.592

AC:

9026

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.487

AC:

1684

AN:

3460

East Asian (EAS)

AF:

0.617

AC:

3173

AN:

5146

South Asian (SAS)

AF:

0.552

AC:

2647

AN:

4794

European-Finnish (FIN)

AF:

0.433

AC:

4547

AN:

10506

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.477

AC:

32386

AN:

67888

Other (OTH)

AF:

0.550

AC:

1156

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1770

3540

5309

7079

8849

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

720

1440

2160

2880

3600

<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:

0.501

Hom.:

41360

Bravo

AF:

0.582

Asia WGS

AF:

0.659

AC:

2292

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.43

(source)

DANN

Benign

0.71

PhyloP100

-1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over