10-15031994-C-T

Variant names:

• chr10-15031994-C-T
• rs2400107
• ENST00000766355.1:n.78+3358G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000766355.1(ENSG00000299781):​n.78+3358G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,646 control chromosomes in the GnomAD database, including 13,804 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 (13804 hom., cov: 29)
• Consequence: ENSG00000299781 ENST00000766355.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 2 publications found

Genes affected

ENSG00000299781 (HGNC:):

DCLRE1CP1 (HGNC:44877): (DNA cross-link repair 1C pseudogene 1)

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766355.1. 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
	DCLRE1CP1	NR_144469.1		n.74+3358G>A		intron	N/A
	ACBD7-DCLRE1CP1	NR_144471.1		n.230-10131G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299781	ENST00000766355.1		n.78+3358G>A		intron	N/A
	ENSG00000299781	ENST00000766356.1		n.106+3358G>A		intron	N/A
	ENSG00000299781	ENST00000766357.1		n.92+3358G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63520 AN: 151524 Hom.: 13799 Cov.: 29

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.442

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.419 AC: 63560 AN: 151646 Hom.: 13804 Cov.: 29 AF XY: 0.424 AC XY: 31425 AN XY: 74050

African (AFR) AF: 0.333 AC: 13758 AN: 41322

American (AMR) AF: 0.371 AC: 5654 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1841 AN: 3456

East Asian (EAS) AF: 0.688 AC: 3484 AN: 5064

South Asian (SAS) AF: 0.638 AC: 3066 AN: 4804

European-Finnish (FIN) AF: 0.444 AC: 4678 AN: 10534

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29471 AN: 67902

Other (OTH) AF: 0.446 AC: 940 AN: 2108

Alfa AF: 0.438 Hom.: 7792

Bravo AF: 0.406

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.23
PhyloP100		-0.65
PromoterAI		0.0053	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2400107; hg19: chr10-15073993;