5-1294893-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2 PM5 BP4_Moderate

The NM_198253.3(TERT):c.97C>G(p.Pro33Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P33S) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 34)
• Consequence: TERT NM_198253.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr5-1294893-G-A is described in ClinVar as [Likely_risk_allele]. Clinvar id is 39127.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {not_provided=1}.
• BP4: Computational evidence support a benign effect (MetaRNN=0.20865524).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TERT	NM_198253.3	c.97C>G	p.Pro33Ala	missense_variant	1/16	ENST00000310581.10
TERT	NM_001193376.3	c.97C>G	p.Pro33Ala	missense_variant	1/15
TERT	NR_149162.3	n.176C>G		non_coding_transcript_exon_variant	1/13
TERT	NR_149163.3	n.176C>G		non_coding_transcript_exon_variant	1/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TERT	ENST00000310581.10	c.97C>G	p.Pro33Ala	missense_variant	1/16	1	NM_198253.3	P2
TERT	ENST00000334602.10	c.97C>G	p.Pro33Ala	missense_variant	1/15	1		A2
TERT	ENST00000460137.6	c.97C>G	p.Pro33Ala	missense_variant, NMD_transcript_variant	1/13	1
TERT	ENST00000656021.1	c.97C>G	p.Pro33Ala	missense_variant, NMD_transcript_variant	1/17

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.071	T
BayesDel_noAF	Benign	-0.34
Cadd	Benign	15
Dann	Benign	0.51
DEOGEN2	Uncertain	0.46	T;.
Eigen	Benign	-0.73
Eigen_PC	Benign	-0.68
FATHMM_MKL	Benign	0.0098	N
LIST_S2	Benign	0.68	T;T
M_CAP	Pathogenic	0.98	D
MetaRNN	Benign	0.21	T;T
MetaSVM	Benign	-0.48	T
MutationAssessor	Benign	1.6	L;L
MutationTaster	Benign	0.82	N;N;N;N
PrimateAI	Pathogenic	0.84	D
PROVEAN	Benign	-1.5	N;N
REVEL	Benign	0.12
Sift	Benign	0.57	T;T
Sift4G	Benign	0.32	T;T
Polyphen		0.0020	B;B
Vest4		0.16
MutPred		0.45		Loss of sheet (P = 0.1501);Loss of sheet (P = 0.1501);
MVP		0.58
MPC		1.0
ClinPred		0.042	T
GERP RS		3.0
Varity_R		0.085
gMVP		0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-1295008;