rs2400107

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-15031994-C-A
• chr10-15031994-C-G
• chr10-15031994-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000766355.1(ENSG00000299781):​n.78+3358G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCLRE1CP1	NR_144469.1	n.74+3358G>T		intron_variant	Intron 1 of 5
ACBD7-DCLRE1CP1	NR_144471.1	n.230-10131G>T		intron_variant	Intron 3 of 7
OLAH	XM_047425423.1	c.-520C>A		upstream_gene_variant			XP_047281379.1
OLAH	XM_024448060.2	c.-520C>A		upstream_gene_variant			XP_024303828.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299781	ENST00000766355.1	n.78+3358G>T		intron_variant	Intron 1 of 2
ENSG00000299781	ENST00000766356.1	n.106+3358G>T		intron_variant	Intron 1 of 5
ENSG00000299781	ENST00000766357.1	n.92+3358G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 7792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.22
PhyloP100		-0.65
PromoterAI		0.0068	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;