14-20377362-A-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_007110.5(TEP1):ā€‹c.6006T>Gā€‹(p.Leu2002=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 1,614,060 control chromosomes in the GnomAD database, including 3,636 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: š‘“ 0.065 ( 375 hom., cov: 32)
Exomes š‘“: 0.065 ( 3261 hom. )

Consequence

TEP1
NM_007110.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.271
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP7
Synonymous conserved (PhyloP=-0.271 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.087 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TEP1NM_007110.5 linkuse as main transcriptc.6006T>G p.Leu2002= synonymous_variant 41/55 ENST00000262715.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TEP1ENST00000262715.10 linkuse as main transcriptc.6006T>G p.Leu2002= synonymous_variant 41/551 NM_007110.5 P1Q99973-1

Frequencies

GnomAD3 genomes
AF:
0.0649
AC:
9870
AN:
152156
Hom.:
374
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0833
Gnomad AMI
AF:
0.0263
Gnomad AMR
AF:
0.0404
Gnomad ASJ
AF:
0.0723
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.0945
Gnomad FIN
AF:
0.0707
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0611
Gnomad OTH
AF:
0.0636
GnomAD3 exomes
AF:
0.0597
AC:
15006
AN:
251364
Hom.:
584
AF XY:
0.0628
AC XY:
8534
AN XY:
135874
show subpopulations
Gnomad AFR exome
AF:
0.0850
Gnomad AMR exome
AF:
0.0303
Gnomad ASJ exome
AF:
0.0761
Gnomad EAS exome
AF:
0.000598
Gnomad SAS exome
AF:
0.0946
Gnomad FIN exome
AF:
0.0708
Gnomad NFE exome
AF:
0.0617
Gnomad OTH exome
AF:
0.0575
GnomAD4 exome
AF:
0.0645
AC:
94329
AN:
1461786
Hom.:
3261
Cov.:
33
AF XY:
0.0656
AC XY:
47737
AN XY:
727204
show subpopulations
Gnomad4 AFR exome
AF:
0.0827
Gnomad4 AMR exome
AF:
0.0320
Gnomad4 ASJ exome
AF:
0.0761
Gnomad4 EAS exome
AF:
0.000327
Gnomad4 SAS exome
AF:
0.0927
Gnomad4 FIN exome
AF:
0.0679
Gnomad4 NFE exome
AF:
0.0651
Gnomad4 OTH exome
AF:
0.0613
GnomAD4 genome
AF:
0.0649
AC:
9877
AN:
152274
Hom.:
375
Cov.:
32
AF XY:
0.0650
AC XY:
4842
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.0833
Gnomad4 AMR
AF:
0.0404
Gnomad4 ASJ
AF:
0.0723
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.0941
Gnomad4 FIN
AF:
0.0707
Gnomad4 NFE
AF:
0.0611
Gnomad4 OTH
AF:
0.0629
Alfa
AF:
0.0640
Hom.:
243
Bravo
AF:
0.0616
Asia WGS
AF:
0.0380
AC:
132
AN:
3474
EpiCase
AF:
0.0632
EpiControl
AF:
0.0627

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.3
DANN
Benign
0.80

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2229101; hg19: chr14-20845521; API