chr19-51346976-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001985.3(ETFB):c.521G>A(p.Arg174His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,608,744 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R174C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001985.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETFB | NM_001985.3 | c.521G>A | p.Arg174His | missense_variant | 5/6 | ENST00000309244.9 | |
ETFB | NM_001014763.1 | c.794G>A | p.Arg265His | missense_variant | 4/5 | ||
ETFB | XM_024451418.2 | c.410G>A | p.Arg137His | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETFB | ENST00000309244.9 | c.521G>A | p.Arg174His | missense_variant | 5/6 | 1 | NM_001985.3 | P1 | |
ENST00000600974.1 | n.78+1730C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00122 AC: 186AN: 152082Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000371 AC: 89AN: 240052Hom.: 0 AF XY: 0.000354 AC XY: 46AN XY: 129774
GnomAD4 exome AF: 0.000145 AC: 211AN: 1456544Hom.: 0 Cov.: 30 AF XY: 0.000133 AC XY: 96AN XY: 723944
GnomAD4 genome AF: 0.00123 AC: 187AN: 152200Hom.: 1 Cov.: 32 AF XY: 0.00118 AC XY: 88AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 07, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 11, 2016 | - - |
Multiple acyl-CoA dehydrogenase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
ETFB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 28, 2022 | 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