rs12039519
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015441.3(OLFML2B):c.*65C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 1,524,914 control chromosomes in the GnomAD database, including 2,688 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.082 ( 1165 hom., cov: 32)
Exomes 𝑓: 0.027 ( 1523 hom. )
Consequence
OLFML2B
NM_015441.3 3_prime_UTR
NM_015441.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0390
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OLFML2B | NM_015441.3 | c.*65C>T | 3_prime_UTR_variant | 8/8 | ENST00000294794.8 | NP_056256.1 | ||
OLFML2B | NM_001347700.2 | c.*65C>T | 3_prime_UTR_variant | 8/8 | NP_001334629.1 | |||
OLFML2B | NM_001297713.2 | c.*65C>T | 3_prime_UTR_variant | 8/8 | NP_001284642.1 | |||
OLFML2B | XM_011509398.3 | c.*65C>T | 3_prime_UTR_variant | 5/5 | XP_011507700.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OLFML2B | ENST00000294794.8 | c.*65C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_015441.3 | ENSP00000294794.3 |
Frequencies
GnomAD3 genomes AF: 0.0819 AC: 12431AN: 151784Hom.: 1166 Cov.: 32
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GnomAD4 exome AF: 0.0273 AC: 37473AN: 1373012Hom.: 1523 Cov.: 26 AF XY: 0.0265 AC XY: 17865AN XY: 675042
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GnomAD4 genome AF: 0.0819 AC: 12444AN: 151902Hom.: 1165 Cov.: 32 AF XY: 0.0797 AC XY: 5911AN XY: 74210
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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