12-10172034-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002543.4(OLR1):c.44C>T(p.Pro15Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,613,636 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002543.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OLR1 | NM_002543.4 | c.44C>T | p.Pro15Leu | missense_variant | 1/6 | ENST00000309539.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OLR1 | ENST00000309539.8 | c.44C>T | p.Pro15Leu | missense_variant | 1/6 | 1 | NM_002543.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251268Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135826
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461522Hom.: 0 Cov.: 29 AF XY: 0.0000688 AC XY: 50AN XY: 727082
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.44C>T (p.P15L) alteration is located in exon 1 (coding exon 1) of the OLR1 gene. This alteration results from a C to T substitution at nucleotide position 44, causing the proline (P) at amino acid position 15 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at