NM_006418.5:c.358-2486C>T

Variant names:

• chr13-53039424-C-T
• rs9568797
• NM_006418.5:c.358-2486C>T

Variant summary

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

The NM_006418.5(OLFM4):​c.358-2486C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 151,904 control chromosomes in the GnomAD database, including 33,060 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 0.66 (33060 hom., cov: 32)
• Consequence: OLFM4 NM_006418.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 6 publications found

Genes affected

OLFM4 (HGNC:17190): (olfactomedin 4) This gene was originally cloned from human myeloblasts and found to be selectively expressed in inflammed colonic epithelium. This gene encodes a member of the olfactomedin family. The encoded protein is an antiapoptotic factor that promotes tumor growth and is an extracellular matrix glycoprotein that facilitates cell adhesion. [provided by RefSeq, Mar 2011]

ENSG00000305297 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006418.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM4	NM_006418.5	MANE Select	c.358-2486C>T		intron	N/A	NP_006409.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLFM4	ENST00000219022.3	TSL:1 MANE Select	c.358-2486C>T		intron	N/A	ENSP00000219022.2
	ENSG00000305297	ENST00000810169.1		n.180-4898G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99553 AN: 151784 Hom.: 33028 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.656 AC: 99633 AN: 151904 Hom.: 33060 Cov.: 32 AF XY: 0.659 AC XY: 48918 AN XY: 74250

African (AFR) AF: 0.613 AC: 25369 AN: 41380

American (AMR) AF: 0.717 AC: 10961 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2552 AN: 3470

East Asian (EAS) AF: 0.932 AC: 4822 AN: 5174

South Asian (SAS) AF: 0.748 AC: 3597 AN: 4810

European-Finnish (FIN) AF: 0.653 AC: 6868 AN: 10524

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43355 AN: 67946

Other (OTH) AF: 0.670 AC: 1414 AN: 2110

Alfa AF: 0.642 Hom.: 47331

Bravo AF: 0.656

Asia WGS AF: 0.792 AC: 2752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9568797; hg19: chr13-53613559;