chr12-101280289-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014503.3(UTP20):c.7A>C(p.Thr3Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000644 in 1,551,608 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 Likely benign (★).
Frequency
Consequence
NM_014503.3 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 |
---|---|---|---|---|---|---|---|
UTP20 | NM_014503.3 | c.7A>C | p.Thr3Pro | missense_variant | 1/62 | ENST00000261637.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTP20 | ENST00000261637.5 | c.7A>C | p.Thr3Pro | missense_variant | 1/62 | 1 | NM_014503.3 | P1 | |
UTP20 | ENST00000551825.1 | n.162A>C | non_coding_transcript_exon_variant | 1/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000640 AC: 1AN: 156348Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 82248
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1399396Hom.: 0 Cov.: 30 AF XY: 0.00000145 AC XY: 1AN XY: 690204
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74366
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 05, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at