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GeneBe

rs2736100

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_198253.3(TERT):c.1574-3777G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151790 control chromosomes in the gnomAD Genomes database, including 20496 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.52 ( 20496 hom., cov: 31)

Consequence

TERT
NM_198253.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter U:1B:1O:3

Conservation

PhyloP100: -1.13

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BP6
?
Variant 5-1286401-C-A is Benign according to our data. Variant chr5-1286401-C-A is described in ClinVar as [Benign]. Clinvar id is 375480. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TERTNM_198253.3 linkuse as main transcriptc.1574-3777G>T intron_variant ENST00000310581.10
TERTNM_001193376.3 linkuse as main transcriptc.1574-3777G>T intron_variant
TERTNR_149162.3 linkuse as main transcriptn.1653-3777G>T intron_variant, non_coding_transcript_variant
TERTNR_149163.3 linkuse as main transcriptn.1653-3777G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TERTENST00000310581.10 linkuse as main transcriptc.1574-3777G>T intron_variant 1 NM_198253.3 P2O14746-1
TERTENST00000334602.10 linkuse as main transcriptc.1574-3777G>T intron_variant 1 A2O14746-3
TERTENST00000460137.6 linkuse as main transcriptc.1574-3777G>T intron_variant, NMD_transcript_variant 1 O14746-4
TERTENST00000656021.1 linkuse as main transcriptc.*883G>T 3_prime_UTR_variant, NMD_transcript_variant 3/17

Frequencies

GnomAD3 genomes
AF:
0.519
AC:
78709
AN:
151790
Hom.:
20496
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.539
Gnomad AMI
AF:
0.469
Gnomad AMR
AF:
0.597
Gnomad ASJ
AF:
0.447
Gnomad EAS
AF:
0.588
Gnomad SAS
AF:
0.411
Gnomad FIN
AF:
0.520
Gnomad MID
AF:
0.311
Gnomad NFE
AF:
0.497
Gnomad OTH
AF:
0.497
Alfa
AF:
0.494
Hom.:
34252
Bravo
AF:
0.528
Asia WGS
AF:
0.469
AC:
1632
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Uncertain:1Benign:1Other:3
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Chronic obstructive pulmonary disease Uncertain:1
Uncertain significance, no assertion criteria providedcase-controlHLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio VillegasMay 04, 2021- -
Idiopathic Pulmonary Fibrosis;C3151443:Dyskeratosis congenita, autosomal dominant 2 Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeNov 04, 2022- -
Interstitial lung disease 2 Other:1
association, no assertion criteria providedcase-controlHLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio VillegasMay 04, 2021- -
Chronic osteomyelitis Other:1
association, no assertion criteria providedcase-controlDepartment of Orthopeadics and Traumatology, Nanfang HospitalSep 01, 2016- -
Combined pulmonary fibrosis-emphysema syndrome Other:1
association, no assertion criteria providedcase-controlHLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio VillegasMay 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.21
Dann
Benign
0.33

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2736100; hg19: chr5-1286516; COSMIC: COSV57244861; COSMIC: COSV57244861; API