rs797045548
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_004826.4(ECEL1):c.1507-9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000814 in 1,597,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004826.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.1507-9G>A | intron_variant | Intron 8 of 17 | ENST00000304546.6 | NP_004817.2 | ||
ECEL1 | NM_001290787.2 | c.1507-9G>A | intron_variant | Intron 8 of 17 | NP_001277716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.1507-9G>A | intron_variant | Intron 8 of 17 | 1 | NM_004826.4 | ENSP00000302051.1 | |||
ECEL1 | ENST00000409941.1 | c.1507-9G>A | intron_variant | Intron 7 of 16 | 1 | ENSP00000386333.1 | ||||
ECEL1 | ENST00000482346.1 | n.1818-9G>A | intron_variant | Intron 7 of 16 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000761 AC: 11AN: 1445014Hom.: 0 Cov.: 34 AF XY: 0.00000279 AC XY: 2AN XY: 717268
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not provided Pathogenic:1
In silico analysis supports a deleterious effect on splicing; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 33672664) -
not specified Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at