rs774027
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003920.5(TIMELESS):c.1363A>T(p.Ile455Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,613,532 control chromosomes in the GnomAD database, including 172,069 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003920.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TIMELESS | NM_003920.5 | c.1363A>T | p.Ile455Leu | missense_variant | 12/29 | ENST00000553532.6 | |
TIMELESS | NM_001330295.2 | c.1360A>T | p.Ile454Leu | missense_variant | 12/29 | ||
TIMELESS | NR_138471.2 | n.1541A>T | non_coding_transcript_exon_variant | 12/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TIMELESS | ENST00000553532.6 | c.1363A>T | p.Ile455Leu | missense_variant | 12/29 | 1 | NM_003920.5 | P4 | |
TIMELESS | ENST00000229201.4 | c.1360A>T | p.Ile454Leu | missense_variant | 12/29 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.423 AC: 64203AN: 151874Hom.: 14825 Cov.: 31
GnomAD3 exomes AF: 0.505 AC: 126268AN: 249882Hom.: 34176 AF XY: 0.500 AC XY: 67559AN XY: 135106
GnomAD4 exome AF: 0.457 AC: 668422AN: 1461540Hom.: 157236 Cov.: 48 AF XY: 0.458 AC XY: 333156AN XY: 727078
GnomAD4 genome ? AF: 0.423 AC: 64231AN: 151992Hom.: 14833 Cov.: 31 AF XY: 0.426 AC XY: 31647AN XY: 74296
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at