chr1-161984843-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015441.3(OLFML2B):āc.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
NM_015441.3 missense
Scores
9
10
Clinical Significance
Conservation
PhyloP100: 4.83
Genes affected
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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.1612A>G | p.Thr538Ala | missense_variant | 7/8 | ENST00000294794.8 | |
OLFML2B | NM_001347700.2 | c.1618A>G | p.Thr540Ala | missense_variant | 7/8 | ||
OLFML2B | NM_001297713.2 | c.1615A>G | p.Thr539Ala | missense_variant | 7/8 | ||
OLFML2B | XM_011509398.3 | c.892A>G | p.Thr298Ala | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OLFML2B | ENST00000294794.8 | c.1612A>G | p.Thr538Ala | missense_variant | 7/8 | 1 | NM_015441.3 | P3 | |
OLFML2B | ENST00000367940.2 | c.1615A>G | p.Thr539Ala | missense_variant | 7/8 | 2 | A2 | ||
OLFML2B | ENST00000367938.1 | c.61A>G | p.Thr21Ala | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000594 AC: 9AN: 151638Hom.: 0 Cov.: 28
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251422Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135880
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GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727228
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GnomAD4 genome AF: 0.0000594 AC: 9AN: 151638Hom.: 0 Cov.: 28 AF XY: 0.0000405 AC XY: 3AN XY: 74010
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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 01, 2024 | The c.1612A>G (p.T538A) alteration is located in exon 7 (coding exon 7) of the OLFML2B gene. This alteration results from a A to G substitution at nucleotide position 1612, causing the threonine (T) at amino acid position 538 to be replaced by an alanine (A). 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
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
T;D;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Uncertain
D;D;T
Sift4G
Benign
T;T;T
Polyphen
B;P;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at