19-15949451-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001004465.1(OR10H4):āc.444T>Gā(p.Cys148Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,614,132 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 Likely benign (ā ).
Frequency
Consequence
NM_001004465.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OR10H4 | NM_001004465.1 | c.444T>G | p.Cys148Trp | missense_variant | 1/1 | ENST00000322107.1 | NP_001004465.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OR10H4 | ENST00000322107.1 | c.444T>G | p.Cys148Trp | missense_variant | 1/1 | 6 | NM_001004465.1 | ENSP00000318834.1 | ||
OR10H4 | ENST00000641275.1 | c.411T>G | p.Cys137Trp | missense_variant | 3/3 | ENSP00000494681.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251394Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135860
GnomAD4 exome AF: 0.000109 AC: 159AN: 1461886Hom.: 0 Cov.: 36 AF XY: 0.000113 AC XY: 82AN XY: 727242
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74388
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at