rs55772253
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003361.4(UMOD):c.1372G>T(p.Val458Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 1,613,928 control chromosomes in the GnomAD database, including 509 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V458M) has been classified as Uncertain significance.
Frequency
Consequence
NM_003361.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UMOD | NM_003361.4 | c.1372G>T | p.Val458Leu | missense_variant | 7/11 | ENST00000396138.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UMOD | ENST00000396138.9 | c.1372G>T | p.Val458Leu | missense_variant | 7/11 | 5 | NM_003361.4 | P2 | |
UMOD | ENST00000396134.6 | c.1471G>T | p.Val491Leu | missense_variant | 8/12 | 2 | A2 | ||
UMOD | ENST00000570689.5 | c.1372G>T | p.Val458Leu | missense_variant | 7/11 | 5 | P2 | ||
UMOD | ENST00000570331.1 | n.137G>T | non_coding_transcript_exon_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0164 AC: 2487AN: 152032Hom.: 35 Cov.: 31
GnomAD3 exomes AF: 0.0208 AC: 5222AN: 251170Hom.: 105 AF XY: 0.0229 AC XY: 3111AN XY: 135774
GnomAD4 exome AF: 0.0222 AC: 32408AN: 1461778Hom.: 475 Cov.: 35 AF XY: 0.0231 AC XY: 16799AN XY: 727180
GnomAD4 genome AF: 0.0163 AC: 2483AN: 152150Hom.: 34 Cov.: 31 AF XY: 0.0161 AC XY: 1196AN XY: 74390
ClinVar
Submissions by phenotype
Familial juvenile hyperuricemic nephropathy type 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 23, 2017 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 14, 2021 | This variant is associated with the following publications: (PMID: 29578190, 22693617, 28609449, 14531790, 26040415) - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 20, 2016 | - - |
Kidney disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Mar 25, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at