13-53039424-C-T

Position:

• chr13-53039424-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLFM4	NM_006418.5	c.358-2486C>T		intron_variant		ENST00000219022.3	NP_006409.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLFM4	ENST00000219022.3	c.358-2486C>T		intron_variant		1	NM_006418.5	ENSP00000219022.2

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

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.670

Alfa AF: 0.641 Hom.: 36938

Bravo AF: 0.656

Asia WGS AF: 0.792 AC: 2752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs9568797; hg19: chr13-53613559;