chr16-69139852-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032830.3(UTP4):c.464C>A(p.Pro155His) variant causes a missense change. The variant allele was found at a frequency of 0.000131 in 1,613,794 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P155P) has been classified as Likely benign.
Frequency
Consequence
NM_032830.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTP4 | NM_032830.3 | c.464C>A | p.Pro155His | missense_variant | 5/17 | ENST00000314423.12 | |
UTP4 | NM_001318391.2 | c.215C>A | p.Pro72His | missense_variant | 5/17 | ||
UTP4 | XM_047434817.1 | c.464C>A | p.Pro155His | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTP4 | ENST00000314423.12 | c.464C>A | p.Pro155His | missense_variant | 5/17 | 1 | NM_032830.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000270 AC: 41AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000298 AC: 75AN: 251474Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135912
GnomAD4 exome AF: 0.000116 AC: 170AN: 1461644Hom.: 1 Cov.: 29 AF XY: 0.000113 AC XY: 82AN XY: 727134
GnomAD4 genome AF: 0.000269 AC: 41AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74402
ClinVar
Submissions by phenotype
UTP4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 26, 2023 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at