11-74001429-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_003356.4(UCP3):c.922C>T(p.Arg308Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,614,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003356.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UCP3 | NM_003356.4 | c.922C>T | p.Arg308Trp | missense_variant | Exon 7 of 7 | ENST00000314032.9 | NP_003347.1 | |
UCP3 | XM_047427519.1 | c.922C>T | p.Arg308Trp | missense_variant | Exon 6 of 6 | XP_047283475.1 | ||
UCP3 | XR_007062495.1 | n.3212C>T | non_coding_transcript_exon_variant | Exon 7 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000322 AC: 81AN: 251476Hom.: 0 AF XY: 0.000228 AC XY: 31AN XY: 135920
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461876Hom.: 0 Cov.: 30 AF XY: 0.0000509 AC XY: 37AN XY: 727242
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
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Obesity Uncertain:1
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UCP3-related disorder Benign:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at