13-53039424-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.649

Publications

6 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OLFM4NM_006418.5 linkc.358-2486C>T intron_variant Intron 2 of 4 ENST00000219022.3 NP_006409.3 Q6UX06A0A024QZ95

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OLFM4ENST00000219022.3 linkc.358-2486C>T intron_variant Intron 2 of 4 1 NM_006418.5 ENSP00000219022.2 Q6UX06
ENSG00000305297ENST00000810169.1 linkn.180-4898G>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.656
AC:
99553
AN:
151784
Hom.:
33028
Cov.:
32
show subpopulations
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
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1756
3512
5268
7024
8780
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
800
1600
2400
3200
4000
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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 v4.3

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

Publications

Other links and lift over

dbSNP: rs9568797; hg19: chr13-53613559; API