chr19-14799455-T-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001370485.4(OR7C1):c.682A>T(p.Ile228Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,613,968 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 1 hom. )
Consequence
OR7C1
NM_001370485.4 missense
NM_001370485.4 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 0.468
Genes affected
OR7C1 (HGNC:8373): (olfactory receptor family 7 subfamily C 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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR7C1 | NM_001370485.4 | c.682A>T | p.Ile228Phe | missense_variant | 5/5 | ENST00000641666.2 | |
OR7C1 | NM_198944.1 | c.682A>T | p.Ile228Phe | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR7C1 | ENST00000641666.2 | c.682A>T | p.Ile228Phe | missense_variant | 5/5 | NM_001370485.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152084Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251204Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135782
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GnomAD4 exome AF: 0.000134 AC: 196AN: 1461884Hom.: 1 Cov.: 32 AF XY: 0.000127 AC XY: 92AN XY: 727240
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GnomAD4 genome AF: 0.000118 AC: 18AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74276
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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 16, 2024 | The c.682A>T (p.I228F) alteration is located in exon 1 (coding exon 1) of the OR7C1 gene. This alteration results from a A to T substitution at nucleotide position 682, causing the isoleucine (I) at amino acid position 228 to be replaced by a phenylalanine (F). 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
Benign
DEOGEN2
Benign
T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;.;.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Uncertain
.;.;.;D
REVEL
Benign
Sift
Uncertain
.;.;.;D
Sift4G
Uncertain
.;.;.;D
Polyphen
D;D;D;D
Vest4
0.32
MVP
0.15
MPC
0.95
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at