1-113987138-A-G

Position:

• chr1-113987138-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLFML3	ENST00000633022.1	n.118+6521A>G		intron_variant, non_coding_transcript_variant		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;