chr1-113987138-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000633022.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFML3	ENST00000633022.1	TSL:4	n.118+6521A>G		intron	N/A

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

African (AFR) AF: 0.533 AC: 22118 AN: 41484

American (AMR) AF: 0.260 AC: 3971 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3470

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5186

South Asian (SAS) AF: 0.282 AC: 1360 AN: 4824

European-Finnish (FIN) AF: 0.292 AC: 3088 AN: 10586

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25321 AN: 67988

Other (OTH) AF: 0.358 AC: 757 AN: 2114

Alfa AF: 0.368 Hom.: 1872

Bravo AF: 0.387

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs11810241; hg19: chr1-114529760;