rs1713440

Variant names:

• chr14-20407110-T-A
• rs1713440
• NM_007110.5:c.568-710A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.89).
• 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 rank	MANE	Protein	UniProt
TEP1	NM_007110.5	c.568-710A>T		intron_variant	Intron 2 of 54	ENST00000262715.10	NP_009041.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEP1	ENST00000262715.10	c.568-710A>T		intron_variant	Intron 2 of 54	1	NM_007110.5	ENSP00000262715.5
TEP1	ENST00000556935.5	c.568-710A>T		intron_variant	Intron 2 of 52	1		ENSP00000452574.1
TEP1	ENST00000555727.5	n.568-710A>T		intron_variant	Intron 2 of 53	1		ENSP00000451634.1

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

African (AFR) AF: 0.751 AC: 31194 AN: 41516

American (AMR) AF: 0.437 AC: 6685 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2142 AN: 5170

South Asian (SAS) AF: 0.522 AC: 2515 AN: 4820

European-Finnish (FIN) AF: 0.362 AC: 3823 AN: 10566

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24177 AN: 67982

Other (OTH) AF: 0.468 AC: 989 AN: 2112

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
PhyloP100		-0.87
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: rs1713440; hg19: chr14-20875269;