rs886037919
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Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The NM_133171.5(ELMO2):c.2080del(p.Leu694TrpfsTer127) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000137 in 1,461,128 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
ELMO2
NM_133171.5 frameshift
NM_133171.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.60
Genes affected
ELMO2 (HGNC:17233): (engulfment and cell motility 2) The protein encoded by this gene interacts with the dedicator of cyto-kinesis 1 protein. Similarity to a C. elegans protein suggests that this protein may function in phagocytosis of apoptotic cells and in cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0384 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 20-46367442-AG-A is Pathogenic according to our data. Variant chr20-46367442-AG-A is described in ClinVar as [Pathogenic]. Clinvar id is 254193.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELMO2 | NM_133171.5 | c.2080del | p.Leu694TrpfsTer127 | frameshift_variant | 22/22 | ENST00000290246.11 | |
LOC124904917 | XR_007067614.1 | n.182+2724del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELMO2 | ENST00000290246.11 | c.2080del | p.Leu694TrpfsTer127 | frameshift_variant | 22/22 | 1 | NM_133171.5 | P4 | |
ENST00000651935.1 | n.151+2724del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250182Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135230
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461128Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726830
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Primary intraosseous venous malformation Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 13, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at