11-4593436-C-T

Variant names:

• chr11-4593436-C-T
• rs1505204
• NM_001405760.1:c.*5571C>T

Variant summary

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

The NM_001405760.1(OR52I2):​c.*5571C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 175,726 control chromosomes in the GnomAD database, including 31,173 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 0.59 (26910 hom., cov: 33)
  • Exomes 𝑓: 0.59 (4263 hom.)
• Consequence: OR52I2 NM_001405760.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 1 publications found

Genes affected

OR52I2 (HGNC:15221): (olfactory receptor family 52 subfamily I 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001405760.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR52I2	NM_001405760.1	MANE Select	c.*5571C>T		downstream_gene	N/A	NP_001392689.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR52I2	ENST00000641896.1	MANE Select	c.*5571C>T		downstream_gene	N/A	ENSP00000493402.1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90223 AN: 151930 Hom.: 26883 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.620

GnomAD4 exome AF: 0.591 AC: 13993 AN: 23678 Hom.: 4263 Cov.: 0 AF XY: 0.591 AC XY: 7391 AN XY: 12508

African (AFR) AF: 0.482 AC: 237 AN: 492

American (AMR) AF: 0.634 AC: 1991 AN: 3142

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 225 AN: 416

East Asian (EAS) AF: 0.587 AC: 1008 AN: 1716

South Asian (SAS) AF: 0.604 AC: 1944 AN: 3218

European-Finnish (FIN) AF: 0.569 AC: 337 AN: 592

Middle Eastern (MID) AF: 0.573 AC: 47 AN: 82

European-Non Finnish (NFE) AF: 0.586 AC: 7570 AN: 12916

Other (OTH) AF: 0.574 AC: 634 AN: 1104

GnomAD4 genome AF: 0.594 AC: 90294 AN: 152048 Hom.: 26910 Cov.: 33 AF XY: 0.597 AC XY: 44390 AN XY: 74330

African (AFR) AF: 0.529 AC: 21910 AN: 41434

American (AMR) AF: 0.648 AC: 9915 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3468

East Asian (EAS) AF: 0.583 AC: 3018 AN: 5174

South Asian (SAS) AF: 0.609 AC: 2933 AN: 4820

European-Finnish (FIN) AF: 0.621 AC: 6553 AN: 10550

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42053 AN: 67992

Other (OTH) AF: 0.617 AC: 1305 AN: 2114

Alfa AF: 0.602 Hom.: 3372

Bravo AF: 0.590

Asia WGS AF: 0.597 AC: 2074 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		-0.16
PromoterAI		-0.0065	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1505204; hg19: chr11-4614666;