chr1-161984884-T-A
Position:
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
NM_015441.3 missense
Scores
1
11
7
Clinical Significance
Conservation
PhyloP100: 0.0700
Genes affected
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 |
---|---|---|---|---|---|---|---|
OLFML2B | NM_015441.3 | c.1571A>T | p.Lys524Met | missense_variant | 7/8 | ENST00000294794.8 | |
OLFML2B | NM_001347700.2 | c.1577A>T | p.Lys526Met | missense_variant | 7/8 | ||
OLFML2B | NM_001297713.2 | c.1574A>T | p.Lys525Met | missense_variant | 7/8 | ||
OLFML2B | XM_011509398.3 | c.851A>T | p.Lys284Met | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OLFML2B | ENST00000294794.8 | c.1571A>T | p.Lys524Met | missense_variant | 7/8 | 1 | NM_015441.3 | P3 | |
OLFML2B | ENST00000367940.2 | c.1574A>T | p.Lys525Met | missense_variant | 7/8 | 2 | A2 | ||
OLFML2B | ENST00000367938.1 | c.20A>T | p.Lys7Met | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 27
GnomAD3 genomes
Cov.:
27
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461834Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727224
GnomAD4 exome
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1
AN:
1461834
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
727224
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 27
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 submitter | clinical testing | Ambry Genetics | Apr 17, 2024 | The 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D;D;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;T
Sift4G
Uncertain
D;D;T
Polyphen
P;P;.
Vest4
MutPred
0.44
.;Loss of methylation at K525 (P = 0.0016);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.