rs377320336
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_020166.5(MCCC1):c.1701G>A(p.Thr567=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T567T) has been classified as Likely benign.
Frequency
Consequence
NM_020166.5 synonymous
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 |
---|---|---|---|---|---|---|---|
MCCC1 | NM_020166.5 | c.1701G>A | p.Thr567= | synonymous_variant | 15/19 | ENST00000265594.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCCC1 | ENST00000265594.9 | c.1701G>A | p.Thr567= | synonymous_variant | 15/19 | 1 | NM_020166.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251368Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135848
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461550Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727100
GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74226
ClinVar
Submissions by phenotype
3-methylcrotonyl-CoA carboxylase 1 deficiency Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Jun 07, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
MCCC1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 15, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at