rs251796
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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.1341-42T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 1,380,914 control chromosomes in the GnomAD database, including 64,761 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.24 ( 5633 hom., cov: 30)
Exomes 𝑓: 0.30 ( 59128 hom. )
Consequence
TERF2
NM_005652.5 intron
NM_005652.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.03
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
?
This place is a probable branch point but likely benign (scored 2 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 16-69361531-A-G is Benign according to our data. Variant chr16-69361531-A-G is described in ClinVar as [Benign]. Clinvar id is 1227895.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERF2 | NM_005652.5 | c.1341-42T>C | intron_variant | ENST00000254942.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERF2 | ENST00000254942.8 | c.1341-42T>C | intron_variant | 1 | NM_005652.5 | P1 | |||
TERF2 | ENST00000567130.1 | n.179-42T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.244 AC: 37055AN: 151582Hom.: 5637 Cov.: 30
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GnomAD3 exomes AF: 0.312 AC: 77990AN: 250350Hom.: 12981 AF XY: 0.314 AC XY: 42461AN XY: 135360
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GnomAD4 exome AF: 0.304 AC: 373523AN: 1229214Hom.: 59128 Cov.: 17 AF XY: 0.304 AC XY: 189740AN XY: 623184
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GnomAD4 genome ? AF: 0.244 AC: 37034AN: 151700Hom.: 5633 Cov.: 30 AF XY: 0.251 AC XY: 18567AN XY: 74116
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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 14, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
BranchPoint Hunter
?
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at