X-131544527-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.454T>Cā(p.Ser152Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000871 in 1,204,864 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 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.454T>C | p.Ser152Pro | missense_variant | 1/1 | ENST00000338616.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR13H1 | ENST00000338616.6 | c.454T>C | p.Ser152Pro | missense_variant | 1/1 | NM_001004486.1 | P1 | ||
IGSF1 | ENST00000370904.6 | c.-913+34141A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000523 AC: 58AN: 110998Hom.: 0 Cov.: 22 AF XY: 0.000543 AC XY: 18AN XY: 33178
GnomAD3 exomes AF: 0.000136 AC: 25AN: 183199Hom.: 0 AF XY: 0.0000738 AC XY: 5AN XY: 67719
GnomAD4 exome AF: 0.0000430 AC: 47AN: 1093813Hom.: 0 Cov.: 35 AF XY: 0.0000251 AC XY: 9AN XY: 359223
GnomAD4 genome AF: 0.000522 AC: 58AN: 111051Hom.: 0 Cov.: 22 AF XY: 0.000541 AC XY: 18AN XY: 33241
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2023 | The c.454T>C (p.S152P) 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 454, causing the serine (S) at amino acid position 152 to be replaced by a proline (P). 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