11-4680280-T-C

Variant names:

• chr11-4680280-T-C
• rs1685
• NM_030774.4:c.*1469A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OR51E2	NM_030774.4	c.*1469A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000396950.4	NP_110401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR51E2	ENST00000396950.4	c.*1469A>G		3_prime_UTR_variant	Exon 2 of 2	6	NM_030774.4	ENSP00000380153.3
OR51E2	ENST00000641638.1	c.*1469A>G		3_prime_UTR_variant	Exon 2 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0201 AC: 834 AN: 41568

American (AMR) AF: 0.0725 AC: 1110 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0815 AC: 283 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0641 AC: 310 AN: 4834

European-Finnish (FIN) AF: 0.0683 AC: 723 AN: 10592

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6750 AN: 68000

Other (OTH) AF: 0.0776 AC: 164 AN: 2114

Alfa AF: 0.0716 Hom.: 251

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
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1685; hg19: chr11-4701510;