dbSNP rs11850456: TEP1:c.4274-41C>T (chr14-20382104-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.4274-41C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 1,611,580 control chromosomes in the GnomAD database, including 4,305 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 0.096 ( 1305 hom., cov: 32)

Exomes 𝑓: 0.041 ( 3000 hom. )

Consequence

TEP1
NM_007110.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

5 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEP1	NM_007110.5 link	c.4274-41C>T		intron_variant	Intron 29 of 54	ENST00000262715.10	NP_009041.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEP1	ENST00000262715.10 link	c.4274-41C>T		intron_variant	Intron 29 of 54	1	NM_007110.5	ENSP00000262715.5

Frequencies

GnomAD3 genomes

AF:

0.0963

AC:

14624

AN:

151890

Hom.:

1299

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.0699

Gnomad FIN

AF:

0.0261

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0247

Gnomad OTH

AF:

0.0938

GnomAD2 exomes

AF:

0.0789

AC:

19455

AN:

246490

AF XY:

0.0704

show subpopulations

Gnomad AFR exome

AF:

0.216

Gnomad AMR exome

AF:

0.210

Gnomad ASJ exome

AF:

0.0177

Gnomad EAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.0237

Gnomad NFE exome

AF:

0.0242

Gnomad OTH exome

AF:

0.0639

GnomAD4 exome

AF:

0.0411

AC:

60006

AN:

1459572

Hom.:

3000

Cov.:

AF XY:

0.0405

AC XY:

29424

AN XY:

725988

show subpopulations

African (AFR)

AF:

0.216

AC:

7225

AN:

33460

American (AMR)

AF:

0.208

AC:

9243

AN:

44458

Ashkenazi Jewish (ASJ)

AF:

0.0187

AC:

483

AN:

25860

East Asian (EAS)

AF:

0.143

AC:

5668

AN:

39662

South Asian (SAS)

AF:

0.0685

AC:

5896

AN:

86012

European-Finnish (FIN)

AF:

0.0224

AC:

1194

AN:

53208

Middle Eastern (MID)

AF:

0.0660

AC:

380

AN:

5758

European-Non Finnish (NFE)

AF:

0.0240

AC:

26671

AN:

1110830

Other (OTH)

AF:

0.0538

AC:

3246

AN:

60324

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

3437

6874

10310

13747

17184

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1324

2648

3972

5296

6620

<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:

0.0964

AC:

14658

AN:

152008

Hom.:

1305

Cov.:

AF XY:

0.0998

AC XY:

7417

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.209

AC:

8668

AN:

41402

American (AMR)

AF:

0.168

AC:

2561

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0153

AC:

AN:

3468

East Asian (EAS)

AF:

0.168

AC:

871

AN:

5172

South Asian (SAS)

AF:

0.0708

AC:

341

AN:

4818

European-Finnish (FIN)

AF:

0.0261

AC:

276

AN:

10588

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0247

AC:

1682

AN:

67982

Other (OTH)

AF:

0.0923

AC:

195

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

581

1162

1743

2324

2905

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0380

Hom.:

441

Bravo

AF:

0.113

Asia WGS

AF:

0.112

AC:

390

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.85

(source)

DANN

Benign

0.24

PhyloP100

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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