chr11-4954915-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001004748.1(OR51A2):c.799G>C(p.Gly267Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 906,878 control chromosomes in the GnomAD database, including 63,850 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2795 hom., cov: 15)
Exomes 𝑓: 0.17 ( 63850 hom. )
Failed GnomAD Quality Control
Consequence
OR51A2
NM_001004748.1 missense
NM_001004748.1 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: -0.0770
Genes affected
OR51A2 (HGNC:14764): (olfactory receptor family 51 subfamily A member 2) 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]
MMP26 (HGNC:14249): (matrix metallopeptidase 26) Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. The encoded preproprotein is proteolytically processed to generate the mature enzyme. This enzyme may degrade collagen type IV, fibronectin, fibrinogen, and beta-casein, and activate matrix metalloproteinase-9 by cleavage. The protein differs from most MMP family members in that it lacks a conserved C-terminal protein domain. The encoded protein may promote cell invasion in multiple human cancers. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0052675903).
BP6
?
Variant 11-4954915-C-G is Benign according to our data. Variant chr11-4954915-C-G is described in ClinVar as [Benign]. Clinvar id is 403274.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR51A2 | NM_001004748.1 | c.799G>C | p.Gly267Arg | missense_variant | 1/1 | ENST00000380371.1 | |
MMP26 | NM_021801.5 | c.-144-33153C>G | intron_variant | ENST00000380390.6 | |||
MMP26 | NM_001384608.1 | c.-152-33355C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR51A2 | ENST00000380371.1 | c.799G>C | p.Gly267Arg | missense_variant | 1/1 | NM_001004748.1 | P1 | ||
MMP26 | ENST00000380390.6 | c.-144-33153C>G | intron_variant | 5 | NM_021801.5 | P1 | |||
MMP26 | ENST00000300762.2 | c.-152-33355C>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 14020AN: 89938Hom.: 2794 Cov.: 15 FAILED QC
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.177 AC: 29634AN: 167744Hom.: 13631 AF XY: 0.169 AC XY: 15315AN XY: 90712
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GnomAD4 exome AF: 0.170 AC: 154226AN: 906878Hom.: 63850 Cov.: 31 AF XY: 0.173 AC XY: 79279AN XY: 458052
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.156 AC: 14032AN: 90044Hom.: 2795 Cov.: 15 AF XY: 0.149 AC XY: 6476AN XY: 43562
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of solvent accessibility (P = 0.0037);
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