chr11-31539685-TC-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019040.5(ELP4):c.284del(p.Ser95TyrfsTer64) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000137 in 1,455,222 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as association (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
ELP4
NM_019040.5 frameshift
NM_019040.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.03
Genes affected
ELP4 (HGNC:1171): (elongator acetyltransferase complex subunit 4) This gene encodes a component of the six subunit elongator complex, a histone acetyltransferase complex that associates directly with RNA polymerase II during transcriptional elongation. The human gene can partially complement sensitivity phenotypes of yeast ELP4 deletion mutants. This gene has also been associated with Rolandic epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP4 | NM_019040.5 | c.284del | p.Ser95TyrfsTer64 | frameshift_variant | 3/10 | ENST00000640961.2 | NP_061913.3 | |
ELP4 | NM_001288726.2 | c.284del | p.Ser95TyrfsTer64 | frameshift_variant | 3/12 | NP_001275655.1 | ||
ELP4 | NM_001288725.2 | c.284del | p.Ser95TyrfsTer64 | frameshift_variant | 3/11 | NP_001275654.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELP4 | ENST00000640961.2 | c.284del | p.Ser95TyrfsTer64 | frameshift_variant | 3/10 | 1 | NM_019040.5 | ENSP00000492152 | P3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.00000814 AC: 2AN: 245550Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133134
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1455222Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 723504
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GnomAD4 genome Cov.: 33
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33
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autism spectrum disorder Other:1
association, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at