chr6-127327134-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001002030.2(ECHDC1):c.231G>A(p.Met77Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,644 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. M77V) 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.231G>A | p.Met77Ile | missense_variant | 3/6 | ENST00000454859.8 | |
LOC105377994 | XR_001744333.2 | n.8292+1858C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECHDC1 | ENST00000454859.8 | c.231G>A | p.Met77Ile | missense_variant | 3/6 | 1 | NM_001002030.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250464Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135304
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460474Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726398
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.249G>A (p.M83I) alteration is located in exon 3 (coding exon 3) of the ECHDC1 gene. This alteration results from a G to A substitution at nucleotide position 249, causing the methionine (M) at amino acid position 83 to be replaced by an isoleucine (I). 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