rs370145267
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_001283009.2(RTEL1):c.1595+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,612,410 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000036 ( 0 hom. )
Consequence
RTEL1
NM_001283009.2 intron
NM_001283009.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0310
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 20-63688059-C-T is Benign according to our data. Variant chr20-63688059-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 473907.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.1595+9C>T | intron_variant | ENST00000360203.11 | |||
RTEL1-TNFRSF6B | NR_037882.1 | n.2422+9C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.1595+9C>T | intron_variant | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152214Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000562 AC: 14AN: 249144Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135368
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GnomAD4 exome AF: 0.0000356 AC: 52AN: 1460196Hom.: 0 Cov.: 33 AF XY: 0.0000372 AC XY: 27AN XY: 726398
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GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74364
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Dyskeratosis congenita, autosomal recessive 5;C4225346:Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | - - |
Dyskeratosis congenita Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Mar 31, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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