rs12279895

chr11-58402523-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001005469.2(OR5B3):c.887A>G(p.Lys296Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,605,970 control chromosomes in the GnomAD database, including 99,988 homozygotes. 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.33 (8304 hom., cov: 32)
  • Exomes 𝑓: 0.35 (91684 hom.)
• Consequence: OR5B3 NM_001005469.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

Genes affected

OR5B3 (HGNC:8324): (olfactory receptor family 5 subfamily B 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0019082725).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR5B3	NM_001005469.2	c.887A>G	p.Lys296Arg	missense_variant	2/2	ENST00000641865.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR5B3	ENST00000641865.1	c.887A>G	p.Lys296Arg	missense_variant	2/2		NM_001005469.2	P1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49989 AN: 151916 Hom.: 8305 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.304

GnomAD3 exomes AF: 0.312 AC: 78260 AN: 251074 Hom.: 12969 AF XY: 0.313 AC XY: 42525 AN XY: 135682

Gnomad AFR exome AF: 0.321

Gnomad AMR exome AF: 0.224

Gnomad ASJ exome AF: 0.333

Gnomad EAS exome AF: 0.137

Gnomad SAS exome AF: 0.285

Gnomad FIN exome AF: 0.333

Gnomad NFE exome AF: 0.366

Gnomad OTH exome AF: 0.321

GnomAD4 exome AF: 0.349 AC: 507755 AN: 1453936 Hom.: 91684 Cov.: 35 AF XY: 0.348 AC XY: 251674 AN XY: 723740

Gnomad4 AFR exome AF: 0.325

Gnomad4 AMR exome AF: 0.230

Gnomad4 ASJ exome AF: 0.335

Gnomad4 EAS exome AF: 0.168

Gnomad4 SAS exome AF: 0.284

Gnomad4 FIN exome AF: 0.335

Gnomad4 NFE exome AF: 0.369

Gnomad4 OTH exome AF: 0.332

GnomAD4 genome AF: 0.329 AC: 50004 AN: 152034 Hom.: 8304 Cov.: 32 AF XY: 0.325 AC XY: 24125 AN XY: 74308

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.302

Alfa AF: 0.350 Hom.: 18279

Bravo AF: 0.321

TwinsUK AF: 0.373 AC: 1382

ALSPAC AF: 0.378 AC: 1457

ESP6500AA AF: 0.328 AC: 1442

ESP6500EA AF: 0.360 AC: 3093

ExAC AF: 0.319 AC: 38693

Asia WGS AF: 0.264 AC: 917 AN: 3478

EpiCase AF: 0.354

EpiControl AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.088
BayesDel_addAF	Benign	-0.77	T
BayesDel_noAF	Benign	-0.73
Cadd	Benign	15
Dann	Uncertain	0.99
DEOGEN2	Benign	0.020	T;T
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.38
FATHMM_MKL	Benign	0.11	N
MetaRNN	Benign	0.0019	T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Uncertain	2.0	M;M
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.20	T
Polyphen		0.34	B;B
Vest4		0.044
MPC		0.040
ClinPred		0.011	T
GERP RS		3.9
Varity_R		0.24
gMVP		0.073

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs12279895; hg19: chr11-58169996; COSMIC: COSV58676611;