12-101286495-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_014503.3(UTP20):c.501G>A(p.Met167Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,610,468 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014503.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UTP20 | NM_014503.3 | c.501G>A | p.Met167Ile | missense_variant | 5/62 | ENST00000261637.5 | NP_055318.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UTP20 | ENST00000261637.5 | c.501G>A | p.Met167Ile | missense_variant | 5/62 | 1 | NM_014503.3 | ENSP00000261637 | P1 | |
UTP20 | ENST00000551825.1 | n.656G>A | non_coding_transcript_exon_variant | 5/8 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00384 AC: 584AN: 152140Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00152 AC: 379AN: 249224Hom.: 0 AF XY: 0.00126 AC XY: 170AN XY: 134788
GnomAD4 exome AF: 0.000798 AC: 1164AN: 1458210Hom.: 2 Cov.: 31 AF XY: 0.000706 AC XY: 512AN XY: 725476
GnomAD4 genome AF: 0.00384 AC: 584AN: 152258Hom.: 4 Cov.: 32 AF XY: 0.00364 AC XY: 271AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at