7-144074455-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001386096.1(OR2A25):āc.236A>Gā(p.Gln79Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,614,132 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_001386096.1 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 | UniProt |
---|---|---|---|---|---|---|---|
OR2A25 | NM_001386096.1 | c.236A>G | p.Gln79Arg | missense_variant | 2/2 | ENST00000641663.1 | |
OR2A25 | NM_001004488.2 | c.236A>G | p.Gln79Arg | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2A25 | ENST00000641663.1 | c.236A>G | p.Gln79Arg | missense_variant | 2/2 | NM_001386096.1 | P1 | ||
OR2A25 | ENST00000408898.2 | c.236A>G | p.Gln79Arg | missense_variant | 1/1 | P1 | |||
OR2A25 | ENST00000641441.1 | c.236A>G | p.Gln79Arg | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251424Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135900
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461836Hom.: 0 Cov.: 54 AF XY: 0.0000949 AC XY: 69AN XY: 727214
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.236A>G (p.Q79R) alteration is located in exon 1 (coding exon 1) of the OR2A25 gene. This alteration results from a A to G substitution at nucleotide position 236, causing the glutamine (Q) at amino acid position 79 to be replaced by an arginine (R). 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