X-131544257-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001004486.1(OR13H1):āc.184T>Cā(p.Phe62Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000232 in 1,208,606 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001004486.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR13H1 | NM_001004486.1 | c.184T>C | p.Phe62Leu | missense_variant | 1/1 | ENST00000338616.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR13H1 | ENST00000338616.6 | c.184T>C | p.Phe62Leu | missense_variant | 1/1 | NM_001004486.1 | P1 | ||
IGSF1 | ENST00000370904.6 | c.-913+34411A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 14AN: 112171Hom.: 0 Cov.: 23 AF XY: 0.0000874 AC XY: 3AN XY: 34325
GnomAD3 exomes AF: 0.0000436 AC: 8AN: 183359Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67821
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1096379Hom.: 0 Cov.: 29 AF XY: 0.0000111 AC XY: 4AN XY: 361755
GnomAD4 genome AF: 0.000125 AC: 14AN: 112227Hom.: 0 Cov.: 23 AF XY: 0.0000872 AC XY: 3AN XY: 34391
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2023 | The c.184T>C (p.F62L) alteration is located in exon 1 (coding exon 1) of the OR13H1 gene. This alteration results from a T to C substitution at nucleotide position 184, causing the phenylalanine (F) at amino acid position 62 to be replaced by a leucine (L). 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