11-4694836-T-C

Position:

• chr11-4694836-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.-51+2817A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,716 control chromosomes in the GnomAD database, including 11,438 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 0.38 (11438 hom., cov: 30)
• Consequence: OR51E2 NM_030774.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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]

OR51C1P (HGNC:15191): (olfactory receptor family 51 subfamily C member 1 pseudogene) 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR51E2	NM_030774.4	c.-51+2817A>G		intron_variant		ENST00000396950.4	NP_110401.1
OR51C1P	NM_001396051.1	c.9+2817A>G		intron_variant		ENST00000641159.2	NP_001382980.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR51E2	ENST00000396950.4	c.-51+2817A>G		intron_variant		6	NM_030774.4	ENSP00000380153.3
OR51C1P	ENST00000641159.2	c.9+2817A>G		intron_variant			NM_001396051.1	ENSP00000497734.1
OR51E2	ENST00000532598.1	c.-130+2817A>G		intron_variant		6		ENSP00000432644.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 57993 AN: 151598 Hom.: 11439 Cov.: 30

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.382 AC: 58018 AN: 151716 Hom.: 11438 Cov.: 30 AF XY: 0.384 AC XY: 28431 AN XY: 74100

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.386

Alfa AF: 0.410 Hom.: 17898

Bravo AF: 0.374

Asia WGS AF: 0.391 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs7108524; hg19: chr11-4716066;