NM_001039702.3:c.342A>G

Variant names:

• chr10-15064442-A-G
• rs10906818
• NM_001039702.3:c.342A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001039702.3(OLAH):​c.342A>G​(p.Leu114Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 1,594,206 control chromosomes in the GnomAD database, including 140,311 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 0.42 (13321 hom., cov: 32)
  • Exomes 𝑓: 0.41 (126990 hom.)
• Consequence: OLAH NM_001039702.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 16 publications found

Genes affected

OLAH (HGNC:25625): (oleoyl-ACP hydrolase) Enables dodecanoyl-[acyl-carrier-protein] hydrolase activity; myristoyl-[acyl-carrier-protein] hydrolase activity; and palmitoyl-[acyl-carrier-protein] hydrolase activity. Involved in medium-chain fatty acid biosynthetic process. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000299798 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039702.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLAH	NM_001039702.3	MANE Select	c.342A>G	p.Leu114Leu	synonymous	Exon 5 of 8	NP_001034791.1
	OLAH	NM_018324.3		c.501A>G	p.Leu167Leu	synonymous	Exon 6 of 9	NP_060794.1
	ACBD7-DCLRE1CP1	NR_144471.1		n.229+7091T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLAH	ENST00000378228.8	TSL:1 MANE Select	c.342A>G	p.Leu114Leu	synonymous	Exon 5 of 8	ENSP00000367473.4
	OLAH	ENST00000378217.3	TSL:2	c.501A>G	p.Leu167Leu	synonymous	Exon 6 of 9	ENSP00000367462.3
	OLAH	ENST00000429028.5	TSL:2	c.342A>G	p.Leu114Leu	synonymous	Exon 5 of 6	ENSP00000399663.1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63076 AN: 151826 Hom.: 13311 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.431

GnomAD2 exomes AF: 0.423 AC: 99965 AN: 236114 AF XY: 0.431

Gnomad AFR exome AF: 0.411

Gnomad AMR exome AF: 0.293

Gnomad ASJ exome AF: 0.449

Gnomad EAS exome AF: 0.591

Gnomad FIN exome AF: 0.370

Gnomad NFE exome AF: 0.413

Gnomad OTH exome AF: 0.428

GnomAD4 exome AF: 0.414 AC: 597649 AN: 1442260 Hom.: 126990 Cov.: 31 AF XY: 0.419 AC XY: 300747 AN XY: 717432

African (AFR) AF: 0.414 AC: 13425 AN: 32450

American (AMR) AF: 0.299 AC: 12279 AN: 41124

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 11790 AN: 25882

East Asian (EAS) AF: 0.640 AC: 24669 AN: 38548

South Asian (SAS) AF: 0.537 AC: 44427 AN: 82704

European-Finnish (FIN) AF: 0.368 AC: 19602 AN: 53240

Middle Eastern (MID) AF: 0.549 AC: 3148 AN: 5736

European-Non Finnish (NFE) AF: 0.401 AC: 442538 AN: 1102856

Other (OTH) AF: 0.432 AC: 25771 AN: 59720

GnomAD4 genome AF: 0.415 AC: 63118 AN: 151946 Hom.: 13321 Cov.: 32 AF XY: 0.413 AC XY: 30666 AN XY: 74270

African (AFR) AF: 0.415 AC: 17215 AN: 41458

American (AMR) AF: 0.353 AC: 5378 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3466

East Asian (EAS) AF: 0.583 AC: 3005 AN: 5150

South Asian (SAS) AF: 0.563 AC: 2713 AN: 4822

European-Finnish (FIN) AF: 0.365 AC: 3858 AN: 10556

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27909 AN: 67928

Other (OTH) AF: 0.437 AC: 922 AN: 2108

Alfa AF: 0.415 Hom.: 20934

Bravo AF: 0.411

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.68
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.23		Position offset: -15

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

Other links and lift over

dbSNP: rs10906818; hg19: chr10-15106441; COSMIC: COSV65492557; COSMIC: COSV65492557;