rs2230786
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_003640.5(ELP1):c.189C>T(p.Leu63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 1,613,842 control chromosomes in the GnomAD database, including 458 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L63L) has been classified as Likely benign.
Frequency
Consequence
NM_003640.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELP1 | NM_003640.5 | c.189C>T | p.Leu63= | synonymous_variant | 3/37 | ENST00000374647.10 | |
ELP1 | XM_047423991.1 | c.189C>T | p.Leu63= | synonymous_variant | 3/25 | ||
ELP1 | NM_001318360.2 | c.-154C>T | 5_prime_UTR_variant | 3/37 | |||
ELP1 | NM_001330749.2 | c.-671C>T | 5_prime_UTR_variant | 3/35 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELP1 | ENST00000374647.10 | c.189C>T | p.Leu63= | synonymous_variant | 3/37 | 1 | NM_003640.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0179 AC: 2723AN: 152166Hom.: 32 Cov.: 32
GnomAD3 exomes AF: 0.0182 AC: 4566AN: 251482Hom.: 67 AF XY: 0.0185 AC XY: 2512AN XY: 135914
GnomAD4 exome AF: 0.0220 AC: 32184AN: 1461558Hom.: 426 Cov.: 31 AF XY: 0.0213 AC XY: 15494AN XY: 727082
GnomAD4 genome ? AF: 0.0179 AC: 2732AN: 152284Hom.: 32 Cov.: 32 AF XY: 0.0180 AC XY: 1339AN XY: 74452
ClinVar
Submissions by phenotype
Familial dysautonomia Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | May 20, 2019 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 28, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 03, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at