rs1713418

Positions:

• chr14-20366650-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007110.5(TEP1):​c.*1787T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,038 control chromosomes in the GnomAD database, including 21,066 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 0.51 (21065 hom., cov: 31)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: TEP1 NM_007110.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEP1	NM_007110.5	c.*1787T>C		3_prime_UTR_variant	55/55	ENST00000262715.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEP1	ENST00000262715.10	c.*1787T>C		3_prime_UTR_variant	55/55	1	NM_007110.5	P1
TEP1	ENST00000553365.5	c.*1231T>C		3_prime_UTR_variant, NMD_transcript_variant	9/9	1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78039 AN: 151914 Hom.: 21037 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.494

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.514 AC: 78110 AN: 152032 Hom.: 21065 Cov.: 31 AF XY: 0.510 AC XY: 37938 AN XY: 74318

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.496

Alfa AF: 0.460 Hom.: 16362

Bravo AF: 0.522

Asia WGS AF: 0.503 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs1713418; hg19: chr14-20834809;