11-6877590-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207186.2(OR10A4):āc.943C>Gā(p.Leu315Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000163 in 1,599,040 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 ).
Frequency
Consequence
NM_207186.2 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 | UniProt |
---|---|---|---|---|---|---|---|
OR10A4 | NM_207186.2 | c.943C>G | p.Leu315Val | missense_variant | 1/1 | ENST00000379829.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR10A4 | ENST00000379829.2 | c.943C>G | p.Leu315Val | missense_variant | 1/1 | NM_207186.2 | P1 | ||
ENST00000637205.2 | n.606-26772G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 25AN: 241694Hom.: 0 AF XY: 0.0000459 AC XY: 6AN XY: 130730
GnomAD4 exome AF: 0.0000173 AC: 25AN: 1446900Hom.: 0 Cov.: 30 AF XY: 0.00000974 AC XY: 7AN XY: 718840
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.943C>G (p.L315V) alteration is located in exon 1 (coding exon 1) of the OR10A4 gene. This alteration results from a C to G substitution at nucleotide position 943, causing the leucine (L) at amino acid position 315 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