rs872072

Variant names:

• chr14-20390854-G-A
• rs872072
• NM_007110.5:c.2256+84C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-20390854-G-A
• chr14-20390854-G-C
• chr14-20390854-G-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.2256+84C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 1,611,362 control chromosomes in the GnomAD database, including 170,397 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 0.54 (24038 hom., cov: 32)
  • Exomes 𝑓: 0.44 (146359 hom.)
• Consequence: TEP1 NM_007110.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEP1	NM_007110.5	c.2256+84C>T		intron_variant	Intron 14 of 54	ENST00000262715.10	NP_009041.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEP1	ENST00000262715.10	c.2256+84C>T		intron_variant	Intron 14 of 54	1	NM_007110.5	ENSP00000262715.5
TEP1	ENST00000556935.5	c.1932+84C>T		intron_variant	Intron 12 of 52	1		ENSP00000452574.1
TEP1	ENST00000555008.5	n.306+84C>T		intron_variant	Intron 2 of 42	1		ENSP00000450541.1
TEP1	ENST00000555727.5	n.2256+84C>T		intron_variant	Intron 14 of 53	1		ENSP00000451634.1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81570 AN: 151934 Hom.: 23985 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.518

GnomAD4 exome AF: 0.442 AC: 644965 AN: 1459310 Hom.: 146359 Cov.: 35 AF XY: 0.441 AC XY: 319912 AN XY: 725708

African (AFR) AF: 0.812 AC: 27151 AN: 33432

American (AMR) AF: 0.441 AC: 19682 AN: 44598

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 13007 AN: 26010

East Asian (EAS) AF: 0.237 AC: 9401 AN: 39652

South Asian (SAS) AF: 0.433 AC: 37262 AN: 86092

European-Finnish (FIN) AF: 0.447 AC: 23846 AN: 53306

Middle Eastern (MID) AF: 0.488 AC: 2810 AN: 5760

European-Non Finnish (NFE) AF: 0.436 AC: 484159 AN: 1110168

Other (OTH) AF: 0.459 AC: 27647 AN: 60292

GnomAD4 genome AF: 0.537 AC: 81682 AN: 152052 Hom.: 24038 Cov.: 32 AF XY: 0.536 AC XY: 39856 AN XY: 74304

African (AFR) AF: 0.798 AC: 33129 AN: 41494

American (AMR) AF: 0.472 AC: 7214 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1770 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5166

South Asian (SAS) AF: 0.442 AC: 2131 AN: 4816

European-Finnish (FIN) AF: 0.460 AC: 4845 AN: 10544

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29477 AN: 67972

Other (OTH) AF: 0.520 AC: 1097 AN: 2110

Alfa AF: 0.444 Hom.: 11481

Bravo AF: 0.548

Asia WGS AF: 0.391 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.82
DANN	Benign	0.32
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs872072; hg19: chr14-20859013; COSMIC: COSV107291829;