chr20-63694757-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001283009.2(RTEL1):c.3126A>C(p.Gln1042His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 1,603,768 control chromosomes in the GnomAD database, including 465,486 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001283009.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.3126A>C | p.Gln1042His | missense_variant | Exon 32 of 35 | 5 | NM_001283009.2 | ENSP00000353332.5 | ||
RTEL1 | ENST00000508582.7 | c.3198A>C | p.Gln1066His | missense_variant | Exon 32 of 35 | 2 | ENSP00000424307.2 | |||
RTEL1 | ENST00000370018.7 | c.3126A>C | p.Gln1042His | missense_variant | Exon 32 of 35 | 1 | ENSP00000359035.3 | |||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.*728A>C | non_coding_transcript_exon_variant | Exon 29 of 35 | 5 | ENSP00000457428.1 | ||||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.*728A>C | 3_prime_UTR_variant | Exon 29 of 35 | 5 | ENSP00000457428.1 |
Frequencies
GnomAD3 genomes AF: 0.806 AC: 122554AN: 152106Hom.: 50397 Cov.: 34
GnomAD3 exomes AF: 0.748 AC: 181757AN: 242878Hom.: 69854 AF XY: 0.749 AC XY: 99279AN XY: 132592
GnomAD4 exome AF: 0.752 AC: 1091745AN: 1451544Hom.: 415032 Cov.: 51 AF XY: 0.752 AC XY: 542105AN XY: 720928
GnomAD4 genome AF: 0.806 AC: 122673AN: 152224Hom.: 50454 Cov.: 34 AF XY: 0.804 AC XY: 59794AN XY: 74408
ClinVar
Submissions by phenotype
not specified Benign:5
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Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
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This variant is classified as Benign based on local population frequency. This variant was detected in 89% of patients studied by a panel of primary immunodeficiencies. Number of patients: 85. Only high quality variants are reported. -
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not provided Benign:4Other:1
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Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
This variant is associated with the following publications: (PMID: 27128385, 23329068) -
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Variant summary: The RTEL1 c.3198A>C (p.Gln1066His) variant involves the alteration of a non-conserved nucleotide that 4/4 in silico tools predict a benign outcome. This variant was found in 87362/115752 control chromosomes (33743 homozygotes) at a frequency of 0.7547343, which indicates that the C allele is the major allele found in the general population. In addition, a clinical diagnostic laboratory classified this variant as benign. Therefore, due to the allele frequency observed in the general control population, the variant of interest has been classified as Benign. -
Dyskeratosis congenita, autosomal recessive 5 Benign:1
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Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 Benign:1
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Dyskeratosis congenita, autosomal recessive 5;C4225346:Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 Benign:1
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Dyskeratosis congenita Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at