GeneBe

rs372147187

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_005652.5(TERF2):​c.*92_*98delTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TERF2
NM_005652.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Publications

0 publications found
Variant links:
Genes affected
TERF2 (HGNC:11729): (telomeric repeat binding factor 2) This gene encodes a telomere specific protein, TERF2, which is a component of the telomere nucleoprotein complex. This protein is present at telomeres in metaphase of the cell cycle, is a second negative regulator of telomere length and plays a key role in the protective activity of telomeres. While having similar telomere binding activity and domain organization, TERF2 differs from TERF1 in that its N terminus is basic rather than acidic. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005652.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TERF2
NM_005652.5
MANE Select
c.*92_*98delTTTTTTT
3_prime_UTR
Exon 10 of 10NP_005643.2Q15554-3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TERF2
ENST00000254942.8
TSL:1 MANE Select
c.*92_*98delTTTTTTT
3_prime_UTR
Exon 10 of 10ENSP00000254942.3Q15554-3
TERF2
ENST00000903039.1
c.*92_*98delTTTTTTT
3_prime_UTR
Exon 10 of 10ENSP00000573098.1
TERF2
ENST00000966429.1
c.*92_*98delTTTTTTT
3_prime_UTR
Exon 10 of 10ENSP00000636488.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000408
AC:
4
AN:
980734
Hom.:
0
AF XY:
0.00000411
AC XY:
2
AN XY:
487198
show subpopulations
African (AFR)
AF:
0.0000476
AC:
1
AN:
21018
American (AMR)
AF:
0.0000514
AC:
1
AN:
19462
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15202
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30030
South Asian (SAS)
AF:
0.00
AC:
0
AN:
52544
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
29710
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3166
European-Non Finnish (NFE)
AF:
0.00000260
AC:
2
AN:
768604
Other (OTH)
AF:
0.00
AC:
0
AN:
40998
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.3

Splicing

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

Publications

Other links and lift over

dbSNP: rs372147187; hg19: chr16-69390702; API