12-56420996-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003920.5(TIMELESS):c.3007A>G(p.Asn1003Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003920.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TIMELESS | NM_003920.5 | c.3007A>G | p.Asn1003Asp | missense_variant | 24/29 | ENST00000553532.6 | |
TIMELESS | NM_001330295.2 | c.3004A>G | p.Asn1002Asp | missense_variant | 24/29 | ||
TIMELESS | NR_138471.2 | n.3144A>G | non_coding_transcript_exon_variant | 24/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TIMELESS | ENST00000553532.6 | c.3007A>G | p.Asn1003Asp | missense_variant | 24/29 | 1 | NM_003920.5 | P4 | |
TIMELESS | ENST00000229201.4 | c.3004A>G | p.Asn1002Asp | missense_variant | 24/29 | 5 | A2 | ||
TIMELESS | ENST00000553314.1 | n.95A>G | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
TIMELESS | ENST00000557589.1 | n.1575A>G | non_coding_transcript_exon_variant | 8/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251440Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135892
GnomAD4 exome AF: 0.0000766 AC: 112AN: 1461886Hom.: 0 Cov.: 37 AF XY: 0.0000743 AC XY: 54AN XY: 727242
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2023 | The c.3007A>G (p.N1003D) alteration is located in exon 24 (coding exon 23) of the TIMELESS gene. This alteration results from a A to G substitution at nucleotide position 3007, causing the asparagine (N) at amino acid position 1003 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at