10-15064442-A-G

Position:

• chr10-15064442-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000378228.8(OLAH):​c.342A>G​(p.Leu114=) 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 ENST00000378228.8 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

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]

ACBD7-DCLRE1CP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLAH	NM_001039702.3	c.342A>G	p.Leu114=	synonymous_variant	5/8	ENST00000378228.8	NP_001034791.1
ACBD7-DCLRE1CP1	NR_144471.1	n.229+7091T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLAH	ENST00000378228.8	c.342A>G	p.Leu114=	synonymous_variant	5/8	1	NM_001039702.3	ENSP00000367473	P1

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

GnomAD3 exomes AF: 0.423 AC: 99965 AN: 236114 Hom.: 21959 AF XY: 0.431 AC XY: 55181 AN XY: 128000

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 SAS exome AF: 0.540

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

Gnomad4 AFR exome AF: 0.414

Gnomad4 AMR exome AF: 0.299

Gnomad4 ASJ exome AF: 0.456

Gnomad4 EAS exome AF: 0.640

Gnomad4 SAS exome AF: 0.537

Gnomad4 FIN exome AF: 0.368

Gnomad4 NFE exome AF: 0.401

Gnomad4 OTH exome AF: 0.432

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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.437

Alfa AF: 0.417 Hom.: 17193

Bravo AF: 0.411

Asia WGS AF: 0.590 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

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