12-56420869-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003920.5(TIMELESS):c.3053C>T(p.Pro1018Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.54 in 1,613,674 control chromosomes in the GnomAD database, including 240,361 homozygotes. In-silico tool predicts 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.3053C>T | p.Pro1018Leu | missense_variant | 25/29 | ENST00000553532.6 | |
TIMELESS | NM_001330295.2 | c.3050C>T | p.Pro1017Leu | missense_variant | 25/29 | ||
TIMELESS | NR_138471.2 | n.3190C>T | non_coding_transcript_exon_variant | 25/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TIMELESS | ENST00000553532.6 | c.3053C>T | p.Pro1018Leu | missense_variant | 25/29 | 1 | NM_003920.5 | P4 | |
TIMELESS | ENST00000229201.4 | c.3050C>T | p.Pro1017Leu | missense_variant | 25/29 | 5 | A2 | ||
TIMELESS | ENST00000553314.1 | n.141C>T | non_coding_transcript_exon_variant | 2/3 | 3 | ||||
TIMELESS | ENST00000557589.1 | n.1621C>T | non_coding_transcript_exon_variant | 9/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.483 AC: 73273AN: 151840Hom.: 18693 Cov.: 31
GnomAD3 exomes AF: 0.491 AC: 123363AN: 251054Hom.: 31813 AF XY: 0.501 AC XY: 67940AN XY: 135674
GnomAD4 exome AF: 0.546 AC: 798009AN: 1461716Hom.: 221659 Cov.: 64 AF XY: 0.546 AC XY: 396746AN XY: 727166
GnomAD4 genome ? AF: 0.482 AC: 73309AN: 151958Hom.: 18702 Cov.: 31 AF XY: 0.485 AC XY: 36037AN XY: 74254
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at