Genetic Variant OPLAH:c.3721-11delC (chr8-144051482-CG-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_017570.5(OPLAH):c.3721-11delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 263,156 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0042 ( 3 hom., cov: 29)

Exomes 𝑓: 0.017 ( 5 hom. )

Consequence

OPLAH
NM_017570.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.23

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 links:

SMPD5 (HGNC:52275): (sphingomyelin phosphodiesterase 5 (pseudogene)) Predicted to enable sphingomyelin phosphodiesterase activity. Predicted to be involved in ceramide biosynthetic process and sphingomyelin catabolic process. Predicted to act upstream of or within ceramide metabolic process. Predicted to be located in endoplasmic reticulum membrane and mitochondrial membrane. [provided by Alliance of Genome Resources, Apr 2022]

SMPD5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 8-144051482-CG-C is Benign according to our data. Variant chr8-144051482-CG-C is described in ClinVar as [Benign]. Clinvar id is 2072722.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00416 (97/23326) while in subpopulation AFR AF= 0.0159 (80/5020). AF 95% confidence interval is 0.0131. There are 3 homozygotes in gnomad4. There are 45 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPLAH	NM_017570.5 link	c.3721-11delC		intron_variant	Intron 26 of 26	ENST00000618853.5	NP_060040.1	O14841

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPLAH	ENST00000618853.5 link	c.3721-11delC		intron_variant	Intron 26 of 26	1	NM_017570.5	ENSP00000480476.1		O14841

Frequencies

GnomAD3 genomes

AF:

0.00416

AC:

AN:

23312

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0160

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00287

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00441

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000954

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000397

Gnomad OTH

AF:

0.00325

GnomAD3 exomes

AF:

0.0361

AC:

1157

AN:

32016

Hom.:

AF XY:

0.0371

AC XY:

682

AN XY:

18390

show subpopulations

Gnomad AFR exome

AF:

0.0491

Gnomad AMR exome

AF:

0.0365

Gnomad ASJ exome

AF:

0.0377

Gnomad EAS exome

AF:

0.0384

Gnomad SAS exome

AF:

0.0370

Gnomad FIN exome

AF:

0.0384

Gnomad NFE exome

AF:

0.0344

Gnomad OTH exome

AF:

0.0391

GnomAD4 exome

AF:

0.0174

AC:

4172

AN:

239830

Hom.:

Cov.:

AF XY:

0.0167

AC XY:

2061

AN XY:

123118

show subpopulations

Gnomad4 AFR exome

AF:

0.0162

Gnomad4 AMR exome

AF:

0.0167

Gnomad4 ASJ exome

AF:

0.0125

Gnomad4 EAS exome

AF:

0.0119

Gnomad4 SAS exome

AF:

0.0118

Gnomad4 FIN exome

AF:

0.00830

Gnomad4 NFE exome

AF:

0.0192

Gnomad4 OTH exome

AF:

0.0141

GnomAD4 genome

AF:

0.00416

AC:

AN:

23326

Hom.:

Cov.:

AF XY:

0.00394

AC XY:

AN XY:

11408

show subpopulations

Gnomad4 AFR

AF:

0.0159

Gnomad4 AMR

AF:

0.00286

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00441

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000954

Gnomad4 NFE

AF:

0.000397

Gnomad4 OTH

AF:

0.00325

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

5-Oxoprolinase deficiency

Benign:1

Aug 10, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over