rs1713440

Positions:

• chr14-20407110-T-A
• chr14-20407110-T-G

Variant summary

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

The NM_007110.5(TEP1):​c.568-710A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,126 control chromosomes in the GnomAD database, including 20,176 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 0.48 (20176 hom., cov: 33)
• Consequence: TEP1 NM_007110.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872

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 = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEP1	NM_007110.5	c.568-710A>T		intron_variant		ENST00000262715.10	NP_009041.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEP1	ENST00000262715.10	c.568-710A>T		intron_variant		1	NM_007110.5	ENSP00000262715	P1
TEP1	ENST00000556935.5	c.568-710A>T		intron_variant		1		ENSP00000452574
TEP1	ENST00000555727.5	c.568-710A>T		intron_variant, NMD_transcript_variant		1		ENSP00000451634

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73453 AN: 152008 Hom.: 20125 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.465

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.484 AC: 73563 AN: 152126 Hom.: 20176 Cov.: 33 AF XY: 0.482 AC XY: 35830 AN XY: 74360

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.468

Alfa AF: 0.413 Hom.: 2055

Bravo AF: 0.499

Asia WGS AF: 0.511 AC: 1776 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	1.2
DANN	Benign	0.63

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: rs1713440; hg19: chr14-20875269;