11-31509799-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_019040.5(ELP4):āc.15A>Cā(p.Ala5Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,614,010 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 Likely benign (ā ).
Frequency
Consequence
NM_019040.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP4 | NM_019040.5 | c.15A>C | p.Ala5Ala | synonymous_variant | Exon 1 of 10 | ENST00000640961.2 | NP_061913.3 | |
ELP4 | NM_001288726.2 | c.15A>C | p.Ala5Ala | synonymous_variant | Exon 1 of 12 | NP_001275655.1 | ||
ELP4 | NM_001288725.2 | c.15A>C | p.Ala5Ala | synonymous_variant | Exon 1 of 11 | NP_001275654.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000562 AC: 14AN: 249286Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135278
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727180
GnomAD4 genome AF: 0.000184 AC: 28AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:1
- -
ELP4-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at