NM_018696.3:c.29C>T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_018696.3(ELAC1):c.29C>T(p.Thr10Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000115 in 1,559,936 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 (★).
Frequency
Consequence
NM_018696.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELAC1 | ENST00000269466.8 | c.29C>T | p.Thr10Met | missense_variant | Exon 2 of 4 | 1 | NM_018696.3 | ENSP00000269466.3 | ||
ENSG00000267699 | ENST00000590722.2 | n.29C>T | non_coding_transcript_exon_variant | Exon 2 of 9 | 2 | ENSP00000465737.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000193 AC: 4AN: 206956Hom.: 0 AF XY: 0.00000900 AC XY: 1AN XY: 111096
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1407838Hom.: 0 Cov.: 30 AF XY: 0.0000129 AC XY: 9AN XY: 696108
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.29C>T (p.T10M) alteration is located in exon 2 (coding exon 1) of the ELAC1 gene. This alteration results from a C to T substitution at nucleotide position 29, causing the threonine (T) at amino acid position 10 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at