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
Not reported in ClinVar
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
Not reported inComputational scores
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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
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MPC
ClinPred
T
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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