X-131544624-T-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001004486.1(OR13H1):c.551T>A(p.Ile184Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000571 in 1,207,847 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 26 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000063 ( 0 hom., 2 hem., cov: 22)
Exomes 𝑓: 0.000057 ( 0 hom. 24 hem. )
Consequence
OR13H1
NM_001004486.1 missense
NM_001004486.1 missense
Scores
3
4
10
Clinical Significance
Conservation
PhyloP100: 1.78
Genes affected
OR13H1 (HGNC:14755): (olfactory receptor family 13 subfamily H member 1) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]
IGSF1 (HGNC:5948): (immunoglobulin superfamily member 1) This gene encodes a member of the immunoglobulin-like domain-containing superfamily. Proteins in this superfamily contain varying numbers of immunoglobulin-like domains and are thought to participate in the regulation of interactions between cells. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Hemizygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR13H1 | NM_001004486.1 | c.551T>A | p.Ile184Asn | missense_variant | 1/1 | ENST00000338616.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR13H1 | ENST00000338616.6 | c.551T>A | p.Ile184Asn | missense_variant | 1/1 | NM_001004486.1 | P1 | ||
IGSF1 | ENST00000370904.6 | c.-913+34044A>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000626 AC: 7AN: 111779Hom.: 0 Cov.: 22 AF XY: 0.0000589 AC XY: 2AN XY: 33939
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GnomAD3 exomes AF: 0.0000656 AC: 12AN: 182792Hom.: 0 AF XY: 0.0000891 AC XY: 6AN XY: 67372
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GnomAD4 exome AF: 0.0000566 AC: 62AN: 1096068Hom.: 0 Cov.: 33 AF XY: 0.0000664 AC XY: 24AN XY: 361472
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GnomAD4 genome AF: 0.0000626 AC: 7AN: 111779Hom.: 0 Cov.: 22 AF XY: 0.0000589 AC XY: 2AN XY: 33939
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | The c.551T>A (p.I184N) alteration is located in exon 1 (coding exon 1) of the OR13H1 gene. This alteration results from a T to A substitution at nucleotide position 551, causing the isoleucine (I) at amino acid position 184 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at