rs10500607

Variant names:

• chr11-4650591-G-A
• rs10500607
• NM_152430.4:c.-39-1897G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152430.4(OR51E1):​c.-39-1897G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,078 control chromosomes in the GnomAD database, including 959 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 0.073 (959 hom., cov: 31)
• Consequence: OR51E1 NM_152430.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 0 publications found

Genes affected

OR51E1 (HGNC:15194): (olfactory receptor family 51 subfamily E member 1) 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR51E1	NM_152430.4	c.-39-1897G>A		intron_variant	Intron 1 of 1	ENST00000396952.6	NP_689643.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR51E1	ENST00000396952.6	c.-39-1897G>A		intron_variant	Intron 1 of 1	6	NM_152430.4	ENSP00000380155.5
OR51E1	ENST00000530215.2	c.-39-1897G>A		intron_variant	Intron 1 of 2	6		ENSP00000431593.1

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 11022 AN: 151960 Hom.: 956 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00426

Gnomad OTH AF: 0.0708

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0726 AC: 11039 AN: 152078 Hom.: 959 Cov.: 31 AF XY: 0.0758 AC XY: 5634 AN XY: 74346

African (AFR) AF: 0.154 AC: 6363 AN: 41440

American (AMR) AF: 0.173 AC: 2643 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1182 AN: 5168

South Asian (SAS) AF: 0.0110 AC: 53 AN: 4814

European-Finnish (FIN) AF: 0.0232 AC: 246 AN: 10586

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00426 AC: 290 AN: 67998

Other (OTH) AF: 0.0705 AC: 149 AN: 2112

Alfa AF: 0.0549 Hom.: 373

Bravo AF: 0.0891

Asia WGS AF: 0.113 AC: 393 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.57
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs10500607; hg19: chr11-4671821;