rs1129332
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002617.4(PEX10):c.*995G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,352 control chromosomes in the GnomAD database, including 5,211 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.25 ( 5206 hom., cov: 34)
Exomes 𝑓: 0.28 ( 5 hom. )
Consequence
PEX10
NM_002617.4 3_prime_UTR
NM_002617.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.43
Genes affected
PEX10 (HGNC:8851): (peroxisomal biogenesis factor 10) This gene encodes a protein involved in import of peroxisomal matrix proteins. This protein localizes to the peroxisomal membrane. Mutations in this gene result in phenotypes within the Zellweger spectrum of peroxisomal biogenesis disorders, ranging from neonatal adrenoleukodystrophy to Zellweger syndrome. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
RER1 (HGNC:30309): (retention in endoplasmic reticulum sorting receptor 1) The protein encoded by this gene is a multi-pass membrane protein that is localized to the golgi apparatus. It is involved in the retention of endoplasmic reticulum (ER) membrane proteins in the ER and retrieval of ER membrane proteins from the early Golgi compartment to facilitate gamma-secretase complex assembly. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEX10 | NM_002617.4 | c.*995G>A | 3_prime_UTR_variant | 6/6 | ENST00000447513.7 | NP_002608.1 | ||
RER1 | NM_007033.5 | c.*1647C>T | 3_prime_UTR_variant | 7/7 | ENST00000605895.6 | NP_008964.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEX10 | ENST00000447513 | c.*995G>A | 3_prime_UTR_variant | 6/6 | 1 | NM_002617.4 | ENSP00000407922.2 | |||
RER1 | ENST00000605895.6 | c.*1647C>T | 3_prime_UTR_variant | 7/7 | 1 | NM_007033.5 | ENSP00000475168.1 |
Frequencies
GnomAD3 genomes AF: 0.246 AC: 37433AN: 152134Hom.: 5205 Cov.: 34
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GnomAD4 exome AF: 0.280 AC: 28AN: 100Hom.: 5 Cov.: 0 AF XY: 0.241 AC XY: 14AN XY: 58
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GnomAD4 genome AF: 0.246 AC: 37437AN: 152252Hom.: 5206 Cov.: 34 AF XY: 0.244 AC XY: 18182AN XY: 74426
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at