rs1713423

chr14-20391914-G-A

Variant summary

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

The NM_007110.5(TEP1):c.1929-147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 777,976 control chromosomes in the GnomAD database, including 102,256 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 0.57 (25330 hom., cov: 30)
  • Exomes 𝑓: 0.49 (76926 hom.)
• Consequence: TEP1 NM_007110.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEP1	NM_007110.5	c.1929-147C>T		intron_variant		ENST00000262715.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEP1	ENST00000262715.10	c.1929-147C>T		intron_variant		1	NM_007110.5	P1
TEP1	ENST00000556935.5	c.1605-147C>T		intron_variant		1
TEP1	ENST00000555727.5	c.1929-147C>T		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85666 AN: 151618 Hom.: 25277 Cov.: 30

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.544

GnomAD4 exome AF: 0.488 AC: 305432 AN: 626240 Hom.: 76926 AF XY: 0.489 AC XY: 157719 AN XY: 322656

Gnomad4 AFR exome AF: 0.742

Gnomad4 AMR exome AF: 0.614

Gnomad4 ASJ exome AF: 0.479

Gnomad4 EAS exome AF: 0.571

Gnomad4 SAS exome AF: 0.547

Gnomad4 FIN exome AF: 0.428

Gnomad4 NFE exome AF: 0.463

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.565 AC: 85775 AN: 151736 Hom.: 25330 Cov.: 30 AF XY: 0.563 AC XY: 41713 AN XY: 74108

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.550

Alfa AF: 0.490 Hom.: 26146

Bravo AF: 0.582

Asia WGS AF: 0.659 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.43
Dann	Benign	0.71

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: rs1713423; hg19: chr14-20860073;