14-20366650-A-G

Variant names:

• chr14-20366650-A-G
• rs1713418
• ENST00000553365.5:n.*1231T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553365.5(TEP1):​n.*1231T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,038 control chromosomes in the GnomAD database, including 21,066 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 0.51 (21065 hom., cov: 31)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: TEP1 ENST00000553365.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 18 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 = 0.691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553365.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEP1	NM_007110.5	MANE Select	c.*1787T>C		3_prime_UTR	Exon 55 of 55	NP_009041.2
	TEP1	NM_001319035.2		c.*1787T>C		3_prime_UTR	Exon 53 of 53	NP_001305964.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEP1	ENST00000553365.5	TSL:1	n.*1231T>C		non_coding_transcript_exon	Exon 9 of 9	ENSP00000450475.1
	TEP1	ENST00000262715.10	TSL:1 MANE Select	c.*1787T>C		3_prime_UTR	Exon 55 of 55	ENSP00000262715.5
	TEP1	ENST00000553365.5	TSL:1	n.*1231T>C		3_prime_UTR	Exon 9 of 9	ENSP00000450475.1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78039 AN: 151914 Hom.: 21037 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.494

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.514 AC: 78110 AN: 152032 Hom.: 21065 Cov.: 31 AF XY: 0.510 AC XY: 37938 AN XY: 74318

African (AFR) AF: 0.697 AC: 28923 AN: 41478

American (AMR) AF: 0.437 AC: 6674 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1631 AN: 3468

East Asian (EAS) AF: 0.422 AC: 2179 AN: 5158

South Asian (SAS) AF: 0.499 AC: 2398 AN: 4808

European-Finnish (FIN) AF: 0.451 AC: 4759 AN: 10562

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 30001 AN: 67966

Other (OTH) AF: 0.496 AC: 1048 AN: 2114

Alfa AF: 0.468 Hom.: 22420

Bravo AF: 0.522

Asia WGS AF: 0.503 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		1.1
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: rs1713418; hg19: chr14-20834809;