chr1-161984884-T-A

Variant summary

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

The NM_015441.3(OLFML2B):​c.1571A>T​(p.Lys524Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,834 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 27)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

OLFML2B
NM_015441.3 missense

Scores

1
11
7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0700
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.1571A>T p.Lys524Met missense_variant 7/8 ENST00000294794.8
OLFML2BNM_001347700.2 linkuse as main transcriptc.1577A>T p.Lys526Met missense_variant 7/8
OLFML2BNM_001297713.2 linkuse as main transcriptc.1574A>T p.Lys525Met missense_variant 7/8
OLFML2BXM_011509398.3 linkuse as main transcriptc.851A>T p.Lys284Met missense_variant 4/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OLFML2BENST00000294794.8 linkuse as main transcriptc.1571A>T p.Lys524Met missense_variant 7/81 NM_015441.3 P3Q68BL8-1
OLFML2BENST00000367940.2 linkuse as main transcriptc.1574A>T p.Lys525Met missense_variant 7/82 A2
OLFML2BENST00000367938.1 linkuse as main transcriptc.20A>T p.Lys7Met missense_variant 1/22 Q68BL8-2

Frequencies

GnomAD3 genomes
Cov.:
27
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461834
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
727224
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:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
27

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsApr 17, 2024The c.1571A>T (p.K524M) alteration is located in exon 7 (coding exon 7) of the OLFML2B gene. This alteration results from a A to T substitution at nucleotide position 1571, causing the lysine (K) at amino acid position 524 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Uncertain
0.13
D
BayesDel_noAF
Uncertain
-0.060
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.54
D;D;.
Eigen
Benign
0.12
Eigen_PC
Benign
0.020
FATHMM_MKL
Benign
0.30
N
LIST_S2
Benign
0.70
T;T;T
M_CAP
Uncertain
0.091
D
MetaRNN
Uncertain
0.44
T;T;T
MetaSVM
Uncertain
0.29
D
MutationAssessor
Uncertain
2.0
M;.;.
MutationTaster
Benign
0.96
D;D;D
PrimateAI
Benign
0.38
T
PROVEAN
Uncertain
-3.4
D;D;D
REVEL
Pathogenic
0.65
Sift
Uncertain
0.0060
D;D;T
Sift4G
Uncertain
0.029
D;D;T
Polyphen
0.95
P;P;.
Vest4
0.48
MutPred
0.44
.;Loss of methylation at K525 (P = 0.0016);.;
MVP
0.84
MPC
0.62
ClinPred
0.96
D
GERP RS
3.2
Varity_R
0.28
gMVP
0.62

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-161954674; API