rs1713423

Variant names:

• chr14-20391914-G-A
• rs1713423
• NM_007110.5:c.1929-147C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TEP1	NM_007110.5	c.1929-147C>T		intron_variant	Intron 12 of 54	ENST00000262715.10	NP_009041.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEP1	ENST00000262715.10	c.1929-147C>T		intron_variant	Intron 12 of 54	1	NM_007110.5	ENSP00000262715.5
TEP1	ENST00000556935.5	c.1605-147C>T		intron_variant	Intron 10 of 52	1		ENSP00000452574.1
TEP1	ENST00000555727.5	n.1929-147C>T		intron_variant	Intron 12 of 53	1		ENSP00000451634.1
TEP1	ENST00000555008.5	n.-169C>T		upstream_gene_variant		1		ENSP00000450541.1

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

African (AFR) AF: 0.742 AC: 11676 AN: 15734

American (AMR) AF: 0.614 AC: 12643 AN: 20576

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 7171 AN: 14958

East Asian (EAS) AF: 0.571 AC: 18200 AN: 31874

South Asian (SAS) AF: 0.547 AC: 27857 AN: 50924

European-Finnish (FIN) AF: 0.428 AC: 14132 AN: 33002

Middle Eastern (MID) AF: 0.453 AC: 1262 AN: 2784

European-Non Finnish (NFE) AF: 0.463 AC: 196661 AN: 424728

Other (OTH) AF: 0.500 AC: 15830 AN: 31660

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

African (AFR) AF: 0.739 AC: 30600 AN: 41382

American (AMR) AF: 0.592 AC: 9026 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1684 AN: 3460

East Asian (EAS) AF: 0.617 AC: 3173 AN: 5146

South Asian (SAS) AF: 0.552 AC: 2647 AN: 4794

European-Finnish (FIN) AF: 0.433 AC: 4547 AN: 10506

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32386 AN: 67888

Other (OTH) AF: 0.550 AC: 1156 AN: 2102

Alfa AF: 0.501 Hom.: 41360

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
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1713423; hg19: chr14-20860073;