5-180739959-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001657.1(OR2Y1):āc.100T>Gā(p.Phe34Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,461,832 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 (ā ).
Frequency
Consequence
NM_001001657.1 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 |
---|---|---|---|---|---|---|---|---|
OR2Y1 | NM_001001657.1 | c.100T>G | p.Phe34Val | missense_variant | 1/1 | ENST00000307832.3 | NP_001001657.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR2Y1 | ENST00000307832.3 | c.100T>G | p.Phe34Val | missense_variant | 1/1 | NM_001001657.1 | ENSP00000312403 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251392Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135888
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461832Hom.: 0 Cov.: 35 AF XY: 0.0000248 AC XY: 18AN XY: 727216
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.100T>G (p.F34V) alteration is located in exon 1 (coding exon 1) of the OR2Y1 gene. This alteration results from a T to G substitution at nucleotide position 100, causing the phenylalanine (F) at amino acid position 34 to be replaced by a valine (V). 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