chr1-55096552-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_015306.3(USP24):c.6007A>G(p.Thr2003Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,613,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015306.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP24 | NM_015306.3 | c.6007A>G | p.Thr2003Ala | missense_variant | 50/68 | ENST00000294383.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP24 | ENST00000294383.7 | c.6007A>G | p.Thr2003Ala | missense_variant | 50/68 | 5 | NM_015306.3 | P1 | |
USP24 | ENST00000484447.6 | c.6007A>G | p.Thr2003Ala | missense_variant | 50/68 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248550Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134856
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1460862Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 726676
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The c.6007A>G (p.T2003A) alteration is located in exon 50 (coding exon 50) of the USP24 gene. This alteration results from a A to G substitution at nucleotide position 6007, causing the threonine (T) at amino acid position 2003 to be replaced by an alanine (A). 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