6-127327136-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001002030.2(ECHDC1):c.229A>G(p.Met77Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,612,266 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M77I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001002030.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECHDC1 | NM_001002030.2 | c.229A>G | p.Met77Val | missense_variant | 3/6 | ENST00000454859.8 | |
LOC105377994 | XR_001744333.2 | n.8292+1860T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECHDC1 | ENST00000454859.8 | c.229A>G | p.Met77Val | missense_variant | 3/6 | 1 | NM_001002030.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249986Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135044
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1460108Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 726160
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 23, 2021 | The c.247A>G (p.M83V) alteration is located in exon 3 (coding exon 3) of the ECHDC1 gene. This alteration results from a A to G substitution at nucleotide position 247, causing the methionine (M) at amino acid position 83 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at