rs2104977

Positions:

• chr14-20370554-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.7317+664C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,168 control chromosomes in the GnomAD database, including 1,361 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 0.12 (1361 hom., cov: 32)
• Consequence: TEP1 NM_007110.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEP1	NM_007110.5	c.7317+664C>T		intron_variant		ENST00000262715.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEP1	ENST00000262715.10	c.7317+664C>T		intron_variant		1	NM_007110.5	P1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18952 AN: 152050 Hom.: 1362 Cov.: 32

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.124 AC: 18939 AN: 152168 Hom.: 1361 Cov.: 32 AF XY: 0.121 AC XY: 8994 AN XY: 74402

Gnomad4 AFR AF: 0.0515

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.124

Alfa AF: 0.156 Hom.: 1712

Bravo AF: 0.121

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.58

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: rs2104977; hg19: chr14-20838713;