1-113994158-C-T

Variant names:

• chr1-113994158-C-T
• rs12029644
• ENST00000633022.1:n.118+13541C>T

Variant summary

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

The ENST00000633022.1(OLFML3):​n.118+13541C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 152,266 control chromosomes in the GnomAD database, including 1,165 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 0.098 (1165 hom., cov: 32)
• Consequence: OLFML3 ENST00000633022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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+13541C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0977 AC: 14864 AN: 152148 Hom.: 1164 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.0923

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0976 AC: 14866 AN: 152266 Hom.: 1165 Cov.: 32 AF XY: 0.103 AC XY: 7639 AN XY: 74444

African (AFR) AF: 0.0227 AC: 942 AN: 41568

American (AMR) AF: 0.153 AC: 2338 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2283 AN: 5168

South Asian (SAS) AF: 0.0930 AC: 449 AN: 4828

European-Finnish (FIN) AF: 0.128 AC: 1358 AN: 10596

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0990 AC: 6733 AN: 68018

Other (OTH) AF: 0.108 AC: 229 AN: 2116

Alfa AF: 0.0952 Hom.: 410

Bravo AF: 0.0992

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.9
DANN	Benign	0.67
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12029644; hg19: chr1-114536780;