rs80227456
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001004482.1(OR13C5):c.244C>T(p.Leu82=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 142,032 control chromosomes in the GnomAD database, including 18,776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L82L) has been classified as Likely benign.
Frequency
Consequence
NM_001004482.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR13C5 | NM_001004482.1 | c.244C>T | p.Leu82= | synonymous_variant | 1/1 | ENST00000374779.3 | |
LOC107987105 | XR_007061705.1 | n.427+22860C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR13C5 | ENST00000374779.3 | c.244C>T | p.Leu82= | synonymous_variant | 1/1 | NM_001004482.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.513 AC: 72829AN: 141916Hom.: 18758 Cov.: 28
GnomAD3 exomes AF: 0.475 AC: 96815AN: 203832Hom.: 26738 AF XY: 0.460 AC XY: 50421AN XY: 109684
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.454 AC: 652646AN: 1439004Hom.: 142549 Cov.: 39 AF XY: 0.454 AC XY: 325276AN XY: 716400
GnomAD4 genome ? AF: 0.513 AC: 72904AN: 142032Hom.: 18776 Cov.: 28 AF XY: 0.518 AC XY: 35942AN XY: 69396
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at