GeneBe

rs72924937

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_002617.4(PEX10):​c.*595G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PEX10
NM_002617.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.423

Publications

0 publications found
Variant links:
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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002617.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PEX10
NM_002617.4
MANE Select
c.*595G>T
3_prime_UTR
Exon 6 of 6NP_002608.1O60683-1
RER1
NM_007033.5
MANE Select
c.*2047C>A
3_prime_UTR
Exon 7 of 7NP_008964.3
PEX10
NM_153818.2
c.*595G>T
3_prime_UTR
Exon 6 of 6NP_722540.1O60683-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PEX10
ENST00000447513.7
TSL:1 MANE Select
c.*595G>T
3_prime_UTR
Exon 6 of 6ENSP00000407922.2O60683-1
RER1
ENST00000605895.6
TSL:1 MANE Select
c.*2047C>A
3_prime_UTR
Exon 7 of 7ENSP00000475168.1O15258
PEX10
ENST00000288774.8
TSL:1
c.*595G>T
3_prime_UTR
Exon 6 of 6ENSP00000288774.3O60683-2

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
27222
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
14534
African (AFR)
AF:
0.00
AC:
0
AN:
380
American (AMR)
AF:
0.00
AC:
0
AN:
3294
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
382
East Asian (EAS)
AF:
0.00
AC:
0
AN:
1612
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4250
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
692
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
86
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
15248
Other (OTH)
AF:
0.00
AC:
0
AN:
1278
GnomAD4 genome
Cov.:
34
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.51
DANN
Benign
0.60
PhyloP100
-0.42
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs72924937; hg19: chr1-2336610; API