rs587778239
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001077706.3(ECT2L):c.1672_1674dup(p.Ile558dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,484 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000053 ( 0 hom. )
Consequence
ECT2L
NM_001077706.3 inframe_insertion
NM_001077706.3 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.390
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_001077706.3. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECT2L | NM_001077706.3 | c.1672_1674dup | p.Ile558dup | inframe_insertion | 15/22 | ENST00000541398.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECT2L | ENST00000541398.7 | c.1672_1674dup | p.Ile558dup | inframe_insertion | 15/22 | 5 | NM_001077706.3 | P1 | |
ECT2L | ENST00000367682.6 | c.1672_1674dup | p.Ile558dup | inframe_insertion | 14/21 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152238Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248468Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134854
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GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461128Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 726856
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GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152356Hom.: 0 Cov.: 31 AF XY: 0.0000268 AC XY: 2AN XY: 74496
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at