rs11810241

Variant names:

• chr1-113987138-A-G
• rs11810241
• ENST00000633022.1:n.118+6521A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000633022.1(OLFML3):​n.118+6521A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,144 control chromosomes in the GnomAD database, including 12,354 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 0.38 (12354 hom., cov: 33)
• Consequence: OLFML3 ENST00000633022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

Genes affected

OLFML3 (HGNC:24956): (olfactomedin like 3) This gene encodes a member of the olfactomedin-like gene family which also includes genes encoding noelin, tiarin, myocilin, amassin, optimedin, photomedin, and latrophilin. The encoded protein is a secreted extracellular matrix glycoprotein with a C-terminal olfactomedin domain that facilitates protein-protein interactions, cell adhesion, and intercellular interactions. It serves as both a scaffold protein that recruits bone morphogenetic protein 1 to its substrate chordin, and as a vascular tissue remodeler with pro-angiogenic properties. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLFML3	ENST00000633022.1	n.118+6521A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58181 AN: 152026 Hom.: 12336 Cov.: 33

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.383 AC: 58238 AN: 152144 Hom.: 12354 Cov.: 33 AF XY: 0.373 AC XY: 27750 AN XY: 74394

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0201

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.358

Alfa AF: 0.363 Hom.: 1764

Bravo AF: 0.387

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11810241; hg19: chr1-114529760;