7-144074883-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001386096.1(OR2A25):āc.664T>Cā(p.Cys222Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,614,004 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C222F) has been classified as Uncertain significance.
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.664T>C | p.Cys222Arg | missense_variant | 2/2 | ENST00000641663.1 | |
OR2A25 | NM_001004488.2 | c.664T>C | p.Cys222Arg | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR2A25 | ENST00000641663.1 | c.664T>C | p.Cys222Arg | missense_variant | 2/2 | NM_001386096.1 | P1 | ||
OR2A25 | ENST00000408898.2 | c.664T>C | p.Cys222Arg | missense_variant | 1/1 | P1 | |||
OR2A25 | ENST00000641441.1 | c.664T>C | p.Cys222Arg | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000759 AC: 19AN: 250262Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135718
GnomAD4 exome AF: 0.000168 AC: 245AN: 1461778Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 127AN XY: 727160
GnomAD4 genome AF: 0.000131 AC: 20AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 16, 2021 | The c.664T>C (p.C222R) alteration is located in exon 1 (coding exon 1) of the OR2A25 gene. This alteration results from a T to C substitution at nucleotide position 664, causing the cysteine (C) at amino acid position 222 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