11-56469720-G-C

Variant names:

• chr11-56469720-G-C
• rs202191066
• NM_001004742.3:c.778C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001004742.3(OR5M3):​c.778C>G​(p.Arg260Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,459,740 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000015 (0 hom.)
• Consequence: OR5M3 NM_001004742.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07796556).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR5M3	NM_001004742.3	c.778C>G	p.Arg260Gly	missense_variant	Exon 2 of 2	ENST00000641993.1	NP_001004742.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR5M3	ENST00000641993.1	c.778C>G	p.Arg260Gly	missense_variant	Exon 2 of 2		NM_001004742.3	ENSP00000493070.1
ENSG00000284732	ENST00000641310.1	c.144+634C>G		intron_variant	Intron 2 of 3			ENSP00000493052.1
ENSG00000284732	ENST00000641599.1	c.144+634C>G		intron_variant	Intron 2 of 2			ENSP00000493241.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000402 AC: 1 AN: 248780 Hom.: 0 AF XY: 0.00000743 AC XY: 1 AN XY: 134540

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000891

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000151 AC: 22 AN: 1459740 Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9 AN XY: 726208

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000198

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	13
DANN	Benign	0.97
DEOGEN2	Benign	0.0063	T;T
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.77
FATHMM_MKL	Benign	0.21	N
LIST_S2	Benign	0.70	.;T
M_CAP	Benign	0.0021	T
MetaRNN	Benign	0.078	T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	0.81	L;L
PrimateAI	Benign	0.20	T
PROVEAN	Benign	-0.77	.;N
REVEL	Benign	0.068
Sift	Uncertain	0.0020	.;D
Sift4G	Uncertain	0.014	.;D
Polyphen		0.047	B;B
Vest4		0.12
MutPred		0.58		Loss of stability (P = 0.0226);Loss of stability (P = 0.0226);
MVP		0.32
MPC		0.12
ClinPred		0.12	T
GERP RS		3.2
Varity_R		0.33
gMVP		0.15

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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

Other links and lift over

dbSNP: rs202191066; hg19: chr11-56237196;