11-56469632-C-T

Position:

• chr11-56469632-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001004742.3(OR5M3):​c.866G>A​(p.Ser289Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: OR5M3 NM_001004742.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.07

Genes affected

OR5M3 (HGNC:14806): (olfactory receptor family 5 subfamily M member 3) 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]

ENSG00000284732 (HGNC:):

ACMG classification

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	Protein	UniProt
OR5M3	NM_001004742.3	c.866G>A	p.Ser289Asn	missense_variant	2/2	ENST00000641993.1	NP_001004742.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR5M3	ENST00000641993.1	c.866G>A	p.Ser289Asn	missense_variant	2/2		NM_001004742.3	ENSP00000493070.1
ENSG00000284732	ENST00000641310.1	c.144+722G>A		intron_variant				ENSP00000493052.1
ENSG00000284732	ENST00000641599.1	c.144+722G>A		intron_variant				ENSP00000493241.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 24

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 01, 2024

The c.866G>A (p.S289N) alteration is located in exon 1 (coding exon 1) of the OR5M3 gene. This alteration results from a G to A substitution at nucleotide position 866, causing the serine (S) at amino acid position 289 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.74
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0079	T;T
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.23
FATHMM_MKL	Benign	0.72	D
LIST_S2	Benign	0.80	.;T
M_CAP	Benign	0.0078	T
MetaRNN	Uncertain	0.50	T;T
MetaSVM	Benign	-0.41	T
MutationAssessor	Pathogenic	2.9	M;M
PrimateAI	Benign	0.20	T
PROVEAN	Uncertain	-2.6	.;D
REVEL	Benign	0.18
Sift	Pathogenic	0.0	.;D
Sift4G	Uncertain	0.0070	.;D
Polyphen		0.97	D;D
Vest4		0.28
MutPred		0.74		Loss of MoRF binding (P = 0.1353);Loss of MoRF binding (P = 0.1353);
MVP		0.53
MPC		0.070
ClinPred		0.98	D
GERP RS		4.1
Varity_R		0.77
gMVP		0.18

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-56237108;