rs181341030
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_014324.6(AMACR):āc.844G>Cā(p.Glu282Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000237 in 1,614,212 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E282D) has been classified as Uncertain significance.
Frequency
Consequence
NM_014324.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMACR | NM_014324.6 | c.844G>C | p.Glu282Gln | missense_variant | 5/5 | ENST00000335606.11 | |
C1QTNF3-AMACR | NR_037951.1 | n.1200G>C | non_coding_transcript_exon_variant | 9/9 | |||
AMACR | NM_001167595.2 | c.844G>C | p.Glu282Gln | missense_variant | 5/6 | ||
AMACR | NM_203382.3 | c.*86G>C | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMACR | ENST00000335606.11 | c.844G>C | p.Glu282Gln | missense_variant | 5/5 | 1 | NM_014324.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000688 AC: 173AN: 251474Hom.: 1 AF XY: 0.000714 AC XY: 97AN XY: 135914
GnomAD4 exome AF: 0.000231 AC: 338AN: 1461874Hom.: 5 Cov.: 32 AF XY: 0.000250 AC XY: 182AN XY: 727236
GnomAD4 genome ? AF: 0.000289 AC: 44AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74514
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 23, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 13, 2014 | - - |
Alpha-methylacyl-CoA racemase deficiency Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Mitochondrial complex I deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | reference population | Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center | Mar 18, 2016 | - - |
Congenital bile acid synthesis defect 4;C3280428:Alpha-methylacyl-CoA racemase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
AMACR-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 08, 2020 | 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