9-108901478-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003640.5(ELP1):c.1961C>A(p.Thr654Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T654T) has been classified as Likely benign.
Frequency
Consequence
NM_003640.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELP1 | NM_003640.5 | c.1961C>A | p.Thr654Lys | missense_variant | 18/37 | ENST00000374647.10 | |
ELP1 | NM_001318360.2 | c.1619C>A | p.Thr540Lys | missense_variant | 18/37 | ||
ELP1 | NM_001330749.2 | c.914C>A | p.Thr305Lys | missense_variant | 16/35 | ||
ELP1 | XM_047423991.1 | c.1961C>A | p.Thr654Lys | missense_variant | 18/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELP1 | ENST00000374647.10 | c.1961C>A | p.Thr654Lys | missense_variant | 18/37 | 1 | NM_003640.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251066Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135652
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461806Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727200
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Familial dysautonomia Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at