rs12340246
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003640.5(ELP1):c.819C>T(p.Leu273=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 1,613,602 control chromosomes in the GnomAD database, including 3,249 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L273L) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELP1 | NM_003640.5 | c.819C>T | p.Leu273= | synonymous_variant | 9/37 | ENST00000374647.10 | |
ELP1 | NM_001318360.2 | c.477C>T | p.Leu159= | synonymous_variant | 9/37 | ||
ELP1 | XM_047423991.1 | c.819C>T | p.Leu273= | synonymous_variant | 9/25 | ||
ELP1 | NM_001330749.2 | c.-229C>T | 5_prime_UTR_variant | 7/35 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELP1 | ENST00000374647.10 | c.819C>T | p.Leu273= | synonymous_variant | 9/37 | 1 | NM_003640.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0513 AC: 7806AN: 152050Hom.: 311 Cov.: 32
GnomAD3 exomes AF: 0.0733 AC: 18430AN: 251476Hom.: 1186 AF XY: 0.0673 AC XY: 9145AN XY: 135914
GnomAD4 exome AF: 0.0528 AC: 77165AN: 1461432Hom.: 2936 Cov.: 33 AF XY: 0.0514 AC XY: 37397AN XY: 727048
GnomAD4 genome AF: 0.0513 AC: 7810AN: 152170Hom.: 313 Cov.: 32 AF XY: 0.0550 AC XY: 4092AN XY: 74384
ClinVar
Submissions by phenotype
Familial dysautonomia Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | May 10, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 13, 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. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
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