rs1538660
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003640.5(ELP1):c.3473C>T(p.Pro1158Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 1,611,346 control chromosomes in the GnomAD database, including 28,307 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1158P) has been classified as Likely benign.
Frequency
Consequence
NM_003640.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELP1 | NM_003640.5 | c.3473C>T | p.Pro1158Leu | missense_variant | 33/37 | ENST00000374647.10 | |
ELP1 | NM_001318360.2 | c.3131C>T | p.Pro1044Leu | missense_variant | 33/37 | ||
ELP1 | NM_001330749.2 | c.2426C>T | p.Pro809Leu | missense_variant | 31/35 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELP1 | ENST00000374647.10 | c.3473C>T | p.Pro1158Leu | missense_variant | 33/37 | 1 | NM_003640.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.217 AC: 33017AN: 151832Hom.: 4003 Cov.: 32
GnomAD3 exomes AF: 0.194 AC: 48749AN: 250972Hom.: 5125 AF XY: 0.194 AC XY: 26290AN XY: 135652
GnomAD4 exome AF: 0.177 AC: 258332AN: 1459392Hom.: 24301 Cov.: 31 AF XY: 0.179 AC XY: 129759AN XY: 726126
GnomAD4 genome ? AF: 0.217 AC: 33039AN: 151954Hom.: 4006 Cov.: 32 AF XY: 0.218 AC XY: 16182AN XY: 74226
ClinVar
Submissions by phenotype
Familial dysautonomia Benign:3
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. - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | May 10, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at