rs1049951
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1
The NM_004092.4(ECHS1):c.224C>T(p.Thr75Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 1,612,138 control chromosomes in the GnomAD database, including 695,367 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004092.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECHS1 | NM_004092.4 | c.224C>T | p.Thr75Ile | missense_variant | 2/8 | ENST00000368547.4 | NP_004083.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECHS1 | ENST00000368547.4 | c.224C>T | p.Thr75Ile | missense_variant | 2/8 | 1 | NM_004092.4 | ENSP00000357535.3 |
Frequencies
GnomAD3 genomes AF: 0.828 AC: 126054AN: 152178Hom.: 54810 Cov.: 35
GnomAD3 exomes AF: 0.919 AC: 228032AN: 248164Hom.: 106241 AF XY: 0.926 AC XY: 124624AN XY: 134650
GnomAD4 exome AF: 0.934 AC: 1363915AN: 1459842Hom.: 640542 Cov.: 70 AF XY: 0.935 AC XY: 679258AN XY: 726128
GnomAD4 genome AF: 0.828 AC: 126101AN: 152296Hom.: 54825 Cov.: 35 AF XY: 0.834 AC XY: 62084AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at