chr22-18078014-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001127649.3(PEX26):c.-363G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00694 in 465,018 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001127649.3 5_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEX26 | NM_001127649.3 | c.-363G>C | 5_prime_UTR_variant | Exon 1 of 5 | ENST00000399744.8 | NP_001121121.1 | ||
PEX26 | NM_017929.6 | c.-115G>C | 5_prime_UTR_variant | Exon 1 of 6 | NP_060399.1 | |||
PEX26 | NM_001199319.2 | c.-115G>C | 5_prime_UTR_variant | Exon 1 of 5 | NP_001186248.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEX26 | ENST00000399744 | c.-363G>C | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_001127649.3 | ENSP00000382648.4 | |||
ENSG00000288683 | ENST00000474897.6 | n.-115G>C | non_coding_transcript_exon_variant | Exon 1 of 9 | 5 | ENSP00000434235.2 | ||||
ENSG00000288683 | ENST00000474897.6 | n.-115G>C | 5_prime_UTR_variant | Exon 1 of 9 | 5 | ENSP00000434235.2 |
Frequencies
GnomAD3 genomes AF: 0.0163 AC: 2481AN: 152168Hom.: 59 Cov.: 32
GnomAD4 exome AF: 0.00235 AC: 736AN: 312738Hom.: 15 Cov.: 0 AF XY: 0.00189 AC XY: 334AN XY: 177014
GnomAD4 genome AF: 0.0163 AC: 2489AN: 152280Hom.: 59 Cov.: 32 AF XY: 0.0156 AC XY: 1161AN XY: 74462
ClinVar
Submissions by phenotype
Peroxisome biogenesis disorder 7A (Zellweger) Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at