chr1-161984843-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_015441.3(OLFML2B):ā€‹c.1612A>Gā€‹(p.Thr538Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,613,484 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000059 ( 0 hom., cov: 28)
Exomes š‘“: 0.0000096 ( 0 hom. )

Consequence

OLFML2B
NM_015441.3 missense

Scores

9
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.83
Variant links:
Genes affected
OLFML2B (HGNC:24558): (olfactomedin like 2B) This gene encodes an olfactomedin domain-containing protein. Most olfactomedin domain-containing proteins are secreted glycoproteins. [provided by RefSeq, Dec 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OLFML2BNM_015441.3 linkuse as main transcriptc.1612A>G p.Thr538Ala missense_variant 7/8 ENST00000294794.8
OLFML2BNM_001347700.2 linkuse as main transcriptc.1618A>G p.Thr540Ala missense_variant 7/8
OLFML2BNM_001297713.2 linkuse as main transcriptc.1615A>G p.Thr539Ala missense_variant 7/8
OLFML2BXM_011509398.3 linkuse as main transcriptc.892A>G p.Thr298Ala missense_variant 4/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OLFML2BENST00000294794.8 linkuse as main transcriptc.1612A>G p.Thr538Ala missense_variant 7/81 NM_015441.3 P3Q68BL8-1
OLFML2BENST00000367940.2 linkuse as main transcriptc.1615A>G p.Thr539Ala missense_variant 7/82 A2
OLFML2BENST00000367938.1 linkuse as main transcriptc.61A>G p.Thr21Ala missense_variant 1/22 Q68BL8-2

Frequencies

GnomAD3 genomes
AF:
0.0000594
AC:
9
AN:
151638
Hom.:
0
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.000218
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000119
AC:
3
AN:
251422
Hom.:
0
AF XY:
0.0000147
AC XY:
2
AN XY:
135880
show subpopulations
Gnomad AFR exome
AF:
0.000123
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:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000958
AC:
14
AN:
1461846
Hom.:
0
Cov.:
31
AF XY:
0.00000825
AC XY:
6
AN XY:
727228
show subpopulations
Gnomad4 AFR exome
AF:
0.000388
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000594
AC:
9
AN:
151638
Hom.:
0
Cov.:
28
AF XY:
0.0000405
AC XY:
3
AN XY:
74010
show subpopulations
Gnomad4 AFR
AF:
0.000218
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000329
Hom.:
0
Bravo
AF:
0.0000718
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.21
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.44
T;D;.
Eigen
Benign
0.069
Eigen_PC
Benign
0.14
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Benign
0.78
T;T;T
M_CAP
Uncertain
0.089
D
MetaRNN
Uncertain
0.49
T;T;T
MetaSVM
Uncertain
0.081
D
MutationAssessor
Benign
1.4
L;.;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-2.0
N;N;N
REVEL
Uncertain
0.39
Sift
Uncertain
0.0070
D;D;T
Sift4G
Benign
0.11
T;T;T
Polyphen
0.12
B;P;.
Vest4
0.71
MVP
0.87
MPC
0.33
ClinPred
0.37
T
GERP RS
4.2
Varity_R
0.20
gMVP
0.63

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: rs776291655; hg19: chr1-161954633; API