chr10-125789003-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_000375.3(UROS):āc.663T>Cā(p.Phe221=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 1,612,904 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_000375.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UROS | NM_000375.3 | c.663T>C | p.Phe221= | splice_region_variant, synonymous_variant | 10/10 | ENST00000368797.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UROS | ENST00000368797.10 | c.663T>C | p.Phe221= | splice_region_variant, synonymous_variant | 10/10 | 1 | NM_000375.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00131 AC: 199AN: 152228Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000333 AC: 82AN: 245932Hom.: 0 AF XY: 0.000261 AC XY: 35AN XY: 134054
GnomAD4 exome AF: 0.000120 AC: 175AN: 1460558Hom.: 0 Cov.: 30 AF XY: 0.000111 AC XY: 81AN XY: 726570
GnomAD4 genome AF: 0.00131 AC: 199AN: 152346Hom.: 1 Cov.: 33 AF XY: 0.00138 AC XY: 103AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 26, 2023 | - - |
UROS-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 17, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at