rs138187344

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001005218.3(OR5B21):​c.169A>T​(p.Met57Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M57V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

OR5B21
NM_001005218.3 missense

Scores

3
3
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.18
Variant links:
Genes affected
OR5B21 (HGNC:19616): (olfactory receptor family 5 subfamily B member 21) 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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.23422727).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OR5B21NM_001005218.3 linkc.169A>T p.Met57Leu missense_variant Exon 1 of 1 ENST00000360374.3 NP_001005218.1 A6NL26
LOC105369313XR_007062673.1 linkn.239-2395A>T intron_variant Intron 2 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR5B21ENST00000360374.3 linkc.169A>T p.Met57Leu missense_variant Exon 1 of 1 6 NM_001005218.3 ENSP00000353537.2 A6NL26

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Uncertain
0.054
T
BayesDel_noAF
Benign
-0.16
CADD
Benign
20
DANN
Benign
0.63
DEOGEN2
Benign
0.021
T
Eigen
Benign
-0.44
Eigen_PC
Benign
-0.49
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.79
T
M_CAP
Benign
0.0084
T
MetaRNN
Benign
0.23
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Pathogenic
3.5
M
PrimateAI
Benign
0.27
T
PROVEAN
Uncertain
-2.8
D
REVEL
Benign
0.23
Sift
Uncertain
0.0080
D
Sift4G
Pathogenic
0.0010
D
Polyphen
0.018
B
Vest4
0.39
MutPred
0.52
Gain of helix (P = 0.2294);
MVP
0.14
MPC
0.15
ClinPred
0.92
D
GERP RS
1.4
Varity_R
0.65
gMVP
0.15

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs138187344; hg19: chr11-58275410; API