19-43506853-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014297.5(ETHE1):c.762C>T(p.Ala254=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,284 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 (★). Synonymous variant affecting the same amino acid position (i.e. A254A) has been classified as Likely benign.
Frequency
Consequence
NM_014297.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ETHE1 | NM_014297.5 | c.762C>T | p.Ala254= | synonymous_variant | 7/7 | ENST00000292147.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ETHE1 | ENST00000292147.7 | c.762C>T | p.Ala254= | synonymous_variant | 7/7 | 1 | NM_014297.5 | P1 | |
ETHE1 | ENST00000594342.5 | c.*325C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251386Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135862
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461284Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726950
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Ethylmalonic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 11, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at