chr2-240045602-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173351.2(OR6B3):c.471G>T(p.Met157Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000121 in 1,487,122 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_173351.2 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR6B3 | NM_173351.2 | c.471G>T | p.Met157Ile | missense_variant | 3/3 | ENST00000641019.2 | NP_775486.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR6B3 | ENST00000641019.2 | c.471G>T | p.Met157Ile | missense_variant | 3/3 | NM_173351.2 | ENSP00000493035 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000265 AC: 4AN: 150858Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.00000480 AC: 1AN: 208200Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 113008
GnomAD4 exome AF: 0.0000105 AC: 14AN: 1336264Hom.: 0 Cov.: 20 AF XY: 0.00000897 AC XY: 6AN XY: 668684
GnomAD4 genome AF: 0.0000265 AC: 4AN: 150858Hom.: 0 Cov.: 28 AF XY: 0.0000136 AC XY: 1AN XY: 73590
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.471G>T (p.M157I) alteration is located in exon 1 (coding exon 1) of the OR6B3 gene. This alteration results from a G to T substitution at nucleotide position 471, causing the methionine (M) at amino acid position 157 to be replaced by an isoleucine (I). 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