20-63659310-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001283009.2(RTEL1):c.-93C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 835,946 control chromosomes in the GnomAD database, including 128,547 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001283009.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.-93C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 35 | ENST00000360203.11 | NP_001269938.1 | ||
RTEL1 | NM_001283009.2 | c.-93C>T | 5_prime_UTR_variant | Exon 2 of 35 | ENST00000360203.11 | NP_001269938.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203 | c.-93C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 35 | 5 | NM_001283009.2 | ENSP00000353332.5 | |||
RTEL1 | ENST00000508582 | c.-93C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 35 | 2 | ENSP00000424307.2 | ||||
RTEL1 | ENST00000370018 | c.-93C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 35 | 1 | ENSP00000359035.3 | ||||
RTEL1 | ENST00000360203 | c.-93C>T | 5_prime_UTR_variant | Exon 2 of 35 | 5 | NM_001283009.2 | ENSP00000353332.5 | |||
RTEL1 | ENST00000508582 | c.-93C>T | 5_prime_UTR_variant | Exon 2 of 35 | 2 | ENSP00000424307.2 | ||||
RTEL1 | ENST00000370018 | c.-93C>T | 5_prime_UTR_variant | Exon 2 of 35 | 1 | ENSP00000359035.3 | ||||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.-93C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 35 | 5 | ENSP00000457428.1 | ||||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.-93C>T | non_coding_transcript_exon_variant | Exon 1 of 35 | 5 | ENSP00000457428.1 | ||||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.-93C>T | 5_prime_UTR_variant | Exon 1 of 35 | 5 | ENSP00000457428.1 |
Frequencies
GnomAD3 genomes AF: 0.561 AC: 85327AN: 151972Hom.: 24663 Cov.: 33
GnomAD4 exome AF: 0.537 AC: 367385AN: 683856Hom.: 103867 Cov.: 9 AF XY: 0.533 AC XY: 193787AN XY: 363618
GnomAD4 genome AF: 0.561 AC: 85385AN: 152090Hom.: 24680 Cov.: 33 AF XY: 0.561 AC XY: 41685AN XY: 74352
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is classified as Benign based on local population frequency. This variant was detected in 68% of patients studied by a panel of primary immunodeficiencies. Number of patients: 65. Only high quality variants are reported. -
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at