chr16-69356756-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005652.5(TERF2):c.*142G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00614 in 915,902 control chromosomes in the GnomAD database, including 229 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.025 ( 158 hom., cov: 31)
Exomes 𝑓: 0.0025 ( 71 hom. )
Consequence
TERF2
NM_005652.5 3_prime_UTR
NM_005652.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.187
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 made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 16-69356756-C-T is Benign according to our data. Variant chr16-69356756-C-T is described in ClinVar as [Benign]. Clinvar id is 1281238.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0829 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERF2 | NM_005652.5 | c.*142G>A | 3_prime_UTR_variant | 10/10 | ENST00000254942.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERF2 | ENST00000254942.8 | c.*142G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_005652.5 | P1 | ||
TERF2 | ENST00000566051.1 | c.*221G>A | 3_prime_UTR_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0246 AC: 3701AN: 150568Hom.: 158 Cov.: 31
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GnomAD4 exome AF: 0.00251 AC: 1921AN: 765226Hom.: 71 Cov.: 10 AF XY: 0.00227 AC XY: 877AN XY: 385562
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GnomAD4 genome AF: 0.0246 AC: 3707AN: 150676Hom.: 158 Cov.: 31 AF XY: 0.0240 AC XY: 1766AN XY: 73474
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 27, 2019 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at