NM_001282611.2:c.364G>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001282611.2(OLFM1):​c.364G>T​(p.Val122Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,202 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

OLFM1
NM_001282611.2 missense

Scores

1
5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.93
Variant links:
Genes affected
OLFM1 (HGNC:17187): (olfactomedin 1) This gene product shares extensive sequence similarity with the rat neuronal olfactomedin-related ER localized protein. While the exact function of the encoded protein is not known, its abundant expression in brain suggests that it may have an essential role in nerve tissue. Several alternatively spliced transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.24245307).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OLFM1NM_001282611.2 linkc.364G>T p.Val122Leu missense_variant Exon 3 of 6 ENST00000371793.8 NP_001269540.1 Q99784-1
OLFM1NM_014279.5 linkc.310G>T p.Val104Leu missense_variant Exon 3 of 6 NP_055094.1 Q99784-3Q6IMJ8
OLFM1NM_001282612.1 linkc.283G>T p.Val95Leu missense_variant Exon 3 of 6 NP_001269541.1 Q99784-5
OLFM1NM_006334.4 linkc.310G>T p.Val104Leu missense_variant Exon 3 of 4 NP_006325.1 Q99784-4Q6IMJ7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OLFM1ENST00000371793.8 linkc.364G>T p.Val122Leu missense_variant Exon 3 of 6 3 NM_001282611.2 ENSP00000360858.3 Q99784-1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD3 exomes
AF:
0.00000399
AC:
1
AN:
250934
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135694
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000882
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000205
AC:
3
AN:
1461202
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
726884
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.0000331
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.78
BayesDel_addAF
Benign
-0.037
T
BayesDel_noAF
Benign
-0.29
CADD
Uncertain
24
DANN
Uncertain
0.97
DEOGEN2
Benign
0.036
.;.;T;.;T;.;T;T
Eigen
Benign
0.13
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.96
D;D;D;D;D;D;D;D
M_CAP
Benign
0.0083
T
MetaRNN
Benign
0.24
T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.8
.;.;.;.;.;L;L;.
PrimateAI
Uncertain
0.76
T
PROVEAN
Benign
-1.9
N;N;N;N;N;N;N;N
REVEL
Benign
0.12
Sift
Benign
0.10
T;T;T;T;T;T;T;T
Sift4G
Benign
0.072
T;T;T;T;T;D;T;T
Polyphen
0.85, 0.0090
.;.;.;.;.;P;B;.
Vest4
0.67
MutPred
0.40
.;.;.;.;.;Loss of MoRF binding (P = 0.0885);Loss of MoRF binding (P = 0.0885);.;
MVP
0.24
MPC
1.0
ClinPred
0.56
D
GERP RS
4.6
Varity_R
0.11
gMVP
0.77

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1205344491; hg19: chr9-137987773; API