rs35936107
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003640.5(ELP1):c.1143G>A(p.Val381Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,614,164 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003640.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP1 | NM_003640.5 | c.1143G>A | p.Val381Val | synonymous_variant | Exon 11 of 37 | ENST00000374647.10 | NP_003631.2 | |
ELP1 | NM_001318360.2 | c.801G>A | p.Val267Val | synonymous_variant | Exon 11 of 37 | NP_001305289.1 | ||
ELP1 | NM_001330749.2 | c.96G>A | p.Val32Val | synonymous_variant | Exon 9 of 35 | NP_001317678.1 | ||
ELP1 | XM_047423991.1 | c.1143G>A | p.Val381Val | synonymous_variant | Exon 11 of 25 | XP_047279947.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00195 AC: 296AN: 152160Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000505 AC: 127AN: 251462Hom.: 0 AF XY: 0.000412 AC XY: 56AN XY: 135906
GnomAD4 exome AF: 0.000196 AC: 287AN: 1461886Hom.: 2 Cov.: 32 AF XY: 0.000158 AC XY: 115AN XY: 727240
GnomAD4 genome AF: 0.00195 AC: 297AN: 152278Hom.: 2 Cov.: 32 AF XY: 0.00177 AC XY: 132AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:3
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ELP1: BP4, BP7 -
Familial dysautonomia Benign:1
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not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
ELP1-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