11-6027233-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001388488.1(OR56A1):c.460C>T(p.Arg154Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,614,066 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_001388488.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR56A1 | NM_001388488.1 | c.460C>T | p.Arg154Trp | missense_variant | 2/2 | ENST00000641900.1 | NP_001375417.1 | |
OR56A1 | NM_001001917.5 | c.460C>T | p.Arg154Trp | missense_variant | 2/2 | NP_001001917.3 | ||
LOC107984303 | XR_001748102.2 | n.89+5145G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR56A1 | ENST00000641900.1 | c.460C>T | p.Arg154Trp | missense_variant | 2/2 | NM_001388488.1 | ENSP00000493047.1 | |||
OR56A1 | ENST00000641423.1 | c.460C>T | p.Arg154Trp | missense_variant | 2/2 | ENSP00000493266.1 | ||||
OR56A1 | ENST00000641938.1 | c.460C>T | p.Arg154Trp | missense_variant | 1/1 | ENSP00000493321.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251224Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135782
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461742Hom.: 0 Cov.: 33 AF XY: 0.0000330 AC XY: 24AN XY: 727182
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2024 | The c.472C>T (p.R158W) alteration is located in exon 1 (coding exon 1) of the OR56A1 gene. This alteration results from a C to T substitution at nucleotide position 472, causing the arginine (R) at amino acid position 158 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