chr1-10474960-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_004565.3(PEX14):c.-7C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000622 in 1,607,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004565.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEX14 | ENST00000356607 | c.-7C>T | 5_prime_UTR_variant | Exon 1 of 9 | 1 | NM_004565.3 | ENSP00000349016.4 | |||
PEX14 | ENST00000472851.1 | n.293+2380C>T | intron_variant | Intron 1 of 3 | 3 | |||||
PEX14 | ENST00000491661.2 | c.-22C>T | upstream_gene_variant | 2 | ENSP00000465473.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000888 AC: 21AN: 236398Hom.: 0 AF XY: 0.000132 AC XY: 17AN XY: 128564
GnomAD4 exome AF: 0.0000646 AC: 94AN: 1455264Hom.: 0 Cov.: 30 AF XY: 0.0000843 AC XY: 61AN XY: 723302
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not provided Uncertain:1
- -
PEX14-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at