chr10-11742661-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024693.5(ECHDC3):c.85C>T(p.Arg29Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,098,558 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024693.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECHDC3 | NM_024693.5 | c.85C>T | p.Arg29Cys | missense_variant | Exon 1 of 5 | ENST00000379215.9 | NP_078969.3 | |
ECHDC3 | XM_047425750.1 | c.85C>T | p.Arg29Cys | missense_variant | Exon 1 of 5 | XP_047281706.1 | ||
ECHDC3 | XM_011519689.1 | c.85C>T | p.Arg29Cys | missense_variant | Exon 1 of 4 | XP_011517991.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECHDC3 | ENST00000379215.9 | c.85C>T | p.Arg29Cys | missense_variant | Exon 1 of 5 | 1 | NM_024693.5 | ENSP00000368517.4 | ||
ECHDC3 | ENST00000496136.5 | n.296C>T | non_coding_transcript_exon_variant | Exon 1 of 6 | 1 | |||||
ECHDC3 | ENST00000420401.5 | c.85C>T | p.Arg29Cys | missense_variant | Exon 1 of 4 | 2 | ENSP00000405584.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000100 AC: 11AN: 1098558Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 7AN XY: 523436
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.85C>T (p.R29C) alteration is located in exon 1 (coding exon 1) of the ECHDC3 gene. This alteration results from a C to T substitution at nucleotide position 85, causing the arginine (R) at amino acid position 29 to be replaced by a cysteine (C). 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