20-63678486-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001283009.2(RTEL1):c.1037+140A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 728,936 control chromosomes in the GnomAD database, including 213,549 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.80 ( 49924 hom., cov: 30)
Exomes 𝑓: 0.74 ( 163625 hom. )
Consequence
RTEL1
NM_001283009.2 intron
NM_001283009.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.45
Genes affected
RTEL1 (HGNC:15888): (regulator of telomere elongation helicase 1) This gene encodes a DNA helicase which functions in the stability, protection and elongation of telomeres and interacts with proteins in the shelterin complex known to protect telomeres during DNA replication. Mutations in this gene have been associated with dyskeratosis congenita and Hoyerall-Hreidarsson syndrome. Read-through transcription of this gene into the neighboring downstream gene, which encodes tumor necrosis factor receptor superfamily, member 6b, generates a non-coding transcript. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]
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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=-0.98).
BP6
?
Variant 20-63678486-A-G is Benign according to our data. Variant chr20-63678486-A-G is described in ClinVar as [Benign]. Clinvar id is 1259728.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.1037+140A>G | intron_variant | ENST00000360203.11 | |||
RTEL1-TNFRSF6B | NR_037882.1 | n.1864+140A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.1037+140A>G | intron_variant | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.800 AC: 121584AN: 151900Hom.: 49863 Cov.: 30
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GnomAD4 exome AF: 0.742 AC: 428360AN: 576918Hom.: 163625 AF XY: 0.743 AC XY: 222379AN XY: 299498
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GnomAD4 genome ? AF: 0.801 AC: 121708AN: 152018Hom.: 49924 Cov.: 30 AF XY: 0.797 AC XY: 59201AN XY: 74294
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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 | Nov 12, 2018 | - - |
Computational scores
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Benign
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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