11-124310328-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001002917.2(OR8D1):c.439G>A(p.Ala147Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,613,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001002917.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR8D1 | NM_001002917.2 | c.439G>A | p.Ala147Thr | missense_variant | Exon 3 of 3 | ENST00000641015.1 | NP_001002917.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR8D1 | ENST00000641015.1 | c.439G>A | p.Ala147Thr | missense_variant | Exon 3 of 3 | NM_001002917.2 | ENSP00000493365.1 | |||
OR8D1 | ENST00000357821.2 | c.439G>A | p.Ala147Thr | missense_variant | Exon 1 of 1 | 6 | ENSP00000350474.2 | |||
OR8D1 | ENST00000641897.1 | c.439G>A | p.Ala147Thr | missense_variant | Exon 4 of 4 | ENSP00000493091.1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250326Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135274
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1461466Hom.: 0 Cov.: 37 AF XY: 0.0000358 AC XY: 26AN XY: 727014
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.439G>A (p.A147T) alteration is located in exon 1 (coding exon 1) of the OR8D1 gene. This alteration results from a G to A substitution at nucleotide position 439, causing the alanine (A) at amino acid position 147 to be replaced by a threonine (T). 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