rs1713419

Positions:

• chr14-20366389-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.*2048T>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 0.491 in 152,096 control chromosomes in the GnomAD database, including 18,883 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 0.49 (18883 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TEP1 NM_007110.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEP1	NM_007110.5	c.*2048T>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.*2048T>C		3_prime_UTR_variant	55/55	1	NM_007110.5	P1
TEP1	ENST00000553365.5	c.*1492T>C		3_prime_UTR_variant, NMD_transcript_variant	9/9	1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74678 AN: 151978 Hom.: 18877 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.476

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.491 AC: 74715 AN: 152096 Hom.: 18883 Cov.: 32 AF XY: 0.489 AC XY: 36338 AN XY: 74348

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.477

Alfa AF: 0.453 Hom.: 21204

Bravo AF: 0.496

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.59

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: rs1713419; hg19: chr14-20834548;