2-232480429-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_004826.4(ECEL1):āc.2198T>Cā(p.Leu733Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004826.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.2198T>C | p.Leu733Pro | missense_variant | Exon 17 of 18 | ENST00000304546.6 | NP_004817.2 | |
ECEL1 | NM_001290787.2 | c.2192T>C | p.Leu731Pro | missense_variant | Exon 17 of 18 | NP_001277716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.2198T>C | p.Leu733Pro | missense_variant | Exon 17 of 18 | 1 | NM_004826.4 | ENSP00000302051.1 | ||
ECEL1 | ENST00000409941.1 | c.2192T>C | p.Leu731Pro | missense_variant | Exon 16 of 17 | 1 | ENSP00000386333.1 | |||
ECEL1 | ENST00000411860.5 | c.377T>C | p.Leu126Pro | missense_variant | Exon 5 of 6 | 3 | ENSP00000412683.1 | |||
ECEL1 | ENST00000482346.1 | n.2509T>C | non_coding_transcript_exon_variant | Exon 16 of 17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251246Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135862
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461678Hom.: 0 Cov.: 35 AF XY: 0.0000234 AC XY: 17AN XY: 727158
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
ECEL1-related disorder Uncertain:1
The ECEL1 c.2198T>C variant is predicted to result in the amino acid substitution p.Leu733Pro. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0035% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-233345139-A-G). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at