chr5-1271409-T-C

Variant names:

• chr5-1271409-T-C
• rs11133719
• NM_198253.3:c.2383-205A>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_198253.3(TERT):​c.2383-205A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,270 control chromosomes in the GnomAD database, including 57,604 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.87 (57604 hom., cov: 34)
• Consequence: TERT NM_198253.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.77

Genes affected

TERT (HGNC:11730): (telomerase reverse transcriptase) Telomerase is a ribonucleoprotein polymerase that maintains telomere ends by addition of the telomere repeat TTAGGG. The enzyme consists of a protein component with reverse transcriptase activity, encoded by this gene, and an RNA component which serves as a template for the telomere repeat. Telomerase expression plays a role in cellular senescence, as it is normally repressed in postnatal somatic cells resulting in progressive shortening of telomeres. Deregulation of telomerase expression in somatic cells may be involved in oncogenesis. Studies in mouse suggest that telomerase also participates in chromosomal repair, since de novo synthesis of telomere repeats may occur at double-stranded breaks. Alternatively spliced variants encoding different isoforms of telomerase reverse transcriptase have been identified; the full-length sequence of some variants has not been determined. Alternative splicing at this locus is thought to be one mechanism of regulation of telomerase activity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 5-1271409-T-C is Benign according to our data. Variant chr5-1271409-T-C is described in ClinVar as [Benign]. Clinvar id is 1263545.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TERT	NM_198253.3	c.2383-205A>G		intron_variant	Intron 7 of 15	ENST00000310581.10	NP_937983.2
TERT	NM_001193376.3	c.2383-205A>G		intron_variant	Intron 7 of 14		NP_001180305.1
TERT	NR_149162.3	n.2366-2776A>G		intron_variant	Intron 6 of 12
TERT	NR_149163.3	n.2330-2776A>G		intron_variant	Intron 6 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TERT	ENST00000310581.10	c.2383-205A>G		intron_variant	Intron 7 of 15	1	NM_198253.3	ENSP00000309572.5

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132165 AN: 152152 Hom.: 57539 Cov.: 34

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.869 AC: 132290 AN: 152270 Hom.: 57604 Cov.: 34 AF XY: 0.870 AC XY: 64794 AN XY: 74460

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.878

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.861

Alfa AF: 0.852 Hom.: 17158

Bravo AF: 0.872

Asia WGS AF: 0.831 AC: 2892 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Apr 09, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.78
DANN	Benign	0.32

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

Publications

LitVar

Other links and lift over

dbSNP: rs11133719; hg19: chr5-1271524;