chr11-4640520-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004751.3(OR51D1):c.730C>T(p.Arg244Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,613,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R244R) has been classified as Likely benign.
Frequency
Consequence
NM_001004751.3 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 |
---|---|---|---|---|---|---|---|
OR51D1 | NM_001004751.3 | c.730C>T | p.Arg244Trp | missense_variant | 2/2 | ENST00000641817.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR51D1 | ENST00000641817.1 | c.730C>T | p.Arg244Trp | missense_variant | 2/2 | NM_001004751.3 | P1 | ||
OR51D1 | ENST00000357605.2 | c.730C>T | p.Arg244Trp | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151964Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251288Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135830
GnomAD4 exome AF: 0.0000766 AC: 112AN: 1461744Hom.: 0 Cov.: 35 AF XY: 0.0000908 AC XY: 66AN XY: 727194
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151964Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74178
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 30, 2024 | The c.730C>T (p.R244W) alteration is located in exon 1 (coding exon 1) of the OR51D1 gene. This alteration results from a C to T substitution at nucleotide position 730, causing the arginine (R) at amino acid position 244 to be replaced by a tryptophan (W). 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