dbSNP rs872072: TEP1:c.2256+84C>T (chr14-20390854-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.2256+84C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 1,611,362 control chromosomes in the GnomAD database, including 170,397 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 0.54 ( 24038 hom., cov: 32)

Exomes 𝑓: 0.44 ( 146359 hom. )

Consequence

TEP1
NM_007110.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.288

Publications

14 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 Gene-Disease associations (from GenCC):

cerebral palsy
Inheritance: AD Classification: MODERATE Submitted by: PanelApp Australia

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007110.5. 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
	TEP1	NM_007110.5	MANE Select	c.2256+84C>T		intron	N/A	NP_009041.2
	TEP1	NM_001319035.2		c.1932+84C>T		intron	N/A	NP_001305964.1	G3V5X7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TEP1	ENST00000262715.10	TSL:1 MANE Select	c.2256+84C>T	intron	N/A	ENSP00000262715.5	Q99973-1
TEP1	ENST00000556935.5	TSL:1	c.1932+84C>T	intron	N/A	ENSP00000452574.1	G3V5X7
TEP1	ENST00000555008.5	TSL:1	n.306+84C>T	intron	N/A	ENSP00000450541.1	G3V2A4

Frequencies

GnomAD3 genomes

AF:

0.537

AC:

81570

AN:

151934

Hom.:

23985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.798

Gnomad AMI

AF:

0.447

Gnomad AMR

AF:

0.472

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.443

Gnomad FIN

AF:

0.460

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.518

GnomAD4 exome

AF:

0.442

AC:

644965

AN:

1459310

Hom.:

146359

Cov.:

AF XY:

0.441

AC XY:

319912

AN XY:

725708

show subpopulations

African (AFR)

AF:

0.812

AC:

27151

AN:

33432

American (AMR)

AF:

0.441

AC:

19682

AN:

44598

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

13007

AN:

26010

East Asian (EAS)

AF:

0.237

AC:

9401

AN:

39652

South Asian (SAS)

AF:

0.433

AC:

37262

AN:

86092

European-Finnish (FIN)

AF:

0.447

AC:

23846

AN:

53306

Middle Eastern (MID)

AF:

0.488

AC:

2810

AN:

5760

European-Non Finnish (NFE)

AF:

0.436

AC:

484159

AN:

1110168

Other (OTH)

AF:

0.459

AC:

27647

AN:

60292

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

19349

38699

58048

77398

96747

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14856

29712

44568

59424

74280

<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:

0.537

AC:

81682

AN:

152052

Hom.:

24038

Cov.:

AF XY:

0.536

AC XY:

39856

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.798

AC:

33129

AN:

41494

American (AMR)

AF:

0.472

AC:

7214

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.510

AC:

1770

AN:

3468

East Asian (EAS)

AF:

0.287

AC:

1482

AN:

5166

South Asian (SAS)

AF:

0.442

AC:

2131

AN:

4816

European-Finnish (FIN)

AF:

0.460

AC:

4845

AN:

10544

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.434

AC:

29477

AN:

67972

Other (OTH)

AF:

0.520

AC:

1097

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1762

3523

5285

7046

8808

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

672

1344

2016

2688

3360

<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:

0.444

Hom.:

11481

Bravo

AF:

0.548

Asia WGS

AF:

0.391

AC:

1363

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.82

(source)

DANN

Benign

0.32

PhyloP100

-0.29

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