rs201049444
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004453.4(ETFDH):āc.642T>Cā(p.Ile214=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,605,376 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 Likely benign (ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 31)
Exomes š: 0.000013 ( 0 hom. )
Consequence
ETFDH
NM_004453.4 synonymous
NM_004453.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0650
Genes affected
ETFDH (HGNC:3483): (electron transfer flavoprotein dehydrogenase) This gene encodes a component of the electron-transfer system in mitochondria and is essential for electron transfer from a number of mitochondrial flavin-containing dehydrogenases to the main respiratory chain. Mutations in this gene are associated with glutaric acidemia. Alternatively spliced transcript variants that encode distinct isoforms have been observed. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 4-158690383-T-C is Benign according to our data. Variant chr4-158690383-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 529455.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.065 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETFDH | NM_004453.4 | c.642T>C | p.Ile214= | synonymous_variant | 6/13 | ENST00000511912.6 | |
ETFDH | NM_001281737.2 | c.501T>C | p.Ile167= | synonymous_variant | 5/12 | ||
ETFDH | NM_001281738.1 | c.459T>C | p.Ile153= | synonymous_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETFDH | ENST00000511912.6 | c.642T>C | p.Ile214= | synonymous_variant | 6/13 | 1 | NM_004453.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251408Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135874
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GnomAD4 exome AF: 0.0000131 AC: 19AN: 1453100Hom.: 0 Cov.: 27 AF XY: 0.0000124 AC XY: 9AN XY: 723614
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152276Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74466
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Multiple acyl-CoA dehydrogenase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at