chr1-113992671-C-T

Variant names:

• chr1-113992671-C-T
• rs7520320
• ENST00000633022.1:n.118+12054C>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+12054C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,196 control chromosomes in the GnomAD database, including 1,374 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 0.12 (1374 hom., cov: 32)
• Consequence: OLFML3 ENST00000633022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 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+12054C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18067 AN: 152078 Hom.: 1370 Cov.: 32

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.119 AC: 18078 AN: 152196 Hom.: 1374 Cov.: 32 AF XY: 0.123 AC XY: 9142 AN XY: 74384

African (AFR) AF: 0.0954 AC: 3964 AN: 41536

American (AMR) AF: 0.160 AC: 2450 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2295 AN: 5172

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1362 AN: 10574

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6752 AN: 68018

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.108 Hom.: 3532

Bravo AF: 0.123

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.65
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs7520320; hg19: chr1-114535293;