11-6002857-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001005179.4(OR56A4):c.136A>C(p.Thr46Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,622 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
Frequency
Consequence
NM_001005179.4 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 |
---|---|---|---|---|---|---|---|
OR56A4 | NM_001005179.4 | c.136A>C | p.Thr46Pro | missense_variant | 3/3 | ENST00000641156.1 | |
OR56A3 | XM_047426926.1 | c.*469-863T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR56A4 | ENST00000641156.1 | c.136A>C | p.Thr46Pro | missense_variant | 3/3 | NM_001005179.4 | P1 | ||
OR56A4 | ENST00000330728.4 | c.292A>C | p.Thr98Pro | missense_variant | 1/1 | ||||
OR56A4 | ENST00000641279.1 | c.136A>C | p.Thr46Pro | missense_variant | 1/1 | P1 | |||
OR56A4 | ENST00000641835.1 | c.136A>C | p.Thr46Pro | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 151882Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251230Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135778
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461740Hom.: 1 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727166
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 151882Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74160
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.292A>C (p.T98P) alteration is located in exon 1 (coding exon 1) of the OR56A4 gene. This alteration results from a A to C substitution at nucleotide position 292, causing the threonine (T) at amino acid position 98 to be replaced by a proline (P). 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