11-4680280-T-C

Position:

• chr11-4680280-T-C

Variant summary

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

The NM_030774.4(OR51E2):​c.*1469A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 152,268 control chromosomes in the GnomAD database, including 438 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.

• Frequency:
  • Genomes: 𝑓 0.068 (438 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR51E2 NM_030774.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

OR51E2 (HGNC:15195): (olfactory receptor family 51 subfamily E 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR51E2	NM_030774.4	c.*1469A>G		3_prime_UTR_variant	2/2	ENST00000396950.4	NP_110401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR51E2	ENST00000396950	c.*1469A>G		3_prime_UTR_variant	2/2		NM_030774.4	ENSP00000380153.3
OR51E2	ENST00000641638	c.*1469A>G		3_prime_UTR_variant	2/2			ENSP00000493442.1

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10345 AN: 152150 Hom.: 437 Cov.: 32

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0643

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.0784

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.0679 AC: 10342 AN: 152268 Hom.: 438 Cov.: 32 AF XY: 0.0658 AC XY: 4896 AN XY: 74448

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.0725

Gnomad4 ASJ AF: 0.0815

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0641

Gnomad4 FIN AF: 0.0683

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.0776

Alfa AF: 0.0692 Hom.: 206

Bravo AF: 0.0635

Asia WGS AF: 0.0220 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.25
DANN	Benign	0.78

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

Other links and lift over

dbSNP: rs1685; hg19: chr11-4701510;