X-131544264-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001004486.1(OR13H1):c.191G>A(p.Ser64Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,208,201 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 50 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.191G>A | p.Ser64Asn | missense_variant | 1/1 | ENST00000338616.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR13H1 | ENST00000338616.6 | c.191G>A | p.Ser64Asn | missense_variant | 1/1 | NM_001004486.1 | P1 | ||
IGSF1 | ENST00000370904.6 | c.-913+34404C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000536 AC: 6AN: 111856Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34020
GnomAD3 exomes AF: 0.0000546 AC: 10AN: 183314Hom.: 0 AF XY: 0.0000885 AC XY: 6AN XY: 67802
GnomAD4 exome AF: 0.000125 AC: 137AN: 1096345Hom.: 0 Cov.: 29 AF XY: 0.000138 AC XY: 50AN XY: 361721
GnomAD4 genome AF: 0.0000536 AC: 6AN: 111856Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34020
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.191G>A (p.S64N) alteration is located in exon 1 (coding exon 1) of the OR13H1 gene. This alteration results from a G to A substitution at nucleotide position 191, causing the serine (S) at amino acid position 64 to be replaced by an asparagine (N). 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