GeneBe

rs782568024

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_017570.5(OPLAH):​c.3721-16_3721-11delCCCCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000389 in 257,080 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 29)
Exomes 𝑓: 0.0000039 ( 0 hom. )

Consequence

OPLAH
NM_017570.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.135

Publications

0 publications found
Variant links:
Genes affected
OPLAH (HGNC:8149): (5-oxoprolinase, ATP-hydrolysing) The protein encoded by this gene acts as a homodimer, using ATP hydrolysis to catalyze the conversion of 5-oxo-L-proline to L-glutamate. Defects in this gene are a cause of 5-oxoprolinase deficiency (OPLAHD). [provided by RefSeq, Jun 2012]
OPLAH Gene-Disease associations (from GenCC):
  • 5-oxoprolinase deficiency
    Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017570.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
OPLAH
NM_017570.5
MANE Select
c.3721-16_3721-11delCCCCCC
intron
N/ANP_060040.1O14841

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
OPLAH
ENST00000618853.5
TSL:1 MANE Select
c.3721-16_3721-11delCCCCCC
intron
N/AENSP00000480476.1O14841
OPLAH
ENST00000894965.1
c.3751-16_3751-11delCCCCCC
intron
N/AENSP00000565024.1
OPLAH
ENST00000919620.1
c.3745-16_3745-11delCCCCCC
intron
N/AENSP00000589679.1

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
AF:
0.00000389
AC:
1
AN:
257080
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
131886
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
5552
American (AMR)
AF:
0.00
AC:
0
AN:
8834
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
4866
East Asian (EAS)
AF:
0.00
AC:
0
AN:
10200
South Asian (SAS)
AF:
0.00
AC:
0
AN:
18444
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10520
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
816
European-Non Finnish (NFE)
AF:
0.00000538
AC:
1
AN:
186032
Other (OTH)
AF:
0.00
AC:
0
AN:
11816
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.14

Splicing

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

Publications

Other links and lift over

dbSNP: rs782568024; hg19: chr8-145106383; API