rs9368606

Variant names:

• chr6-29550888-A-C
• rs9368606
• NM_001396058.1:c.6+31A>C

Variant summary

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

The NM_001396058.1(OR2I1):​c.6+31A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,184 control chromosomes in the GnomAD database, including 2,448 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 0.17 (2448 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: OR2I1 NM_001396058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798
• Publications: 10 publications found

Genes affected

OR2I1 (HGNC:8258): (olfactory receptor family 2 subfamily I 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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396058.1. 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
	OR2I1	NM_001396058.1	MANE Select	c.6+31A>C		intron	N/A	NP_001382987.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2I1P	ENST00000641137.2	MANE Select	c.6+31A>C		intron	N/A	ENSP00000493715.1
	OR2I1P	ENST00000641730.1		n.451+31A>C		intron	N/A
	OR2I1P	ENST00000642037.1		n.194+288A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25355 AN: 152066 Hom.: 2446 Cov.: 32

Gnomad AFR AF: 0.0694

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.168

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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.167 AC: 25358 AN: 152184 Hom.: 2448 Cov.: 32 AF XY: 0.171 AC XY: 12753 AN XY: 74404

African (AFR) AF: 0.0692 AC: 2875 AN: 41538

American (AMR) AF: 0.222 AC: 3400 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1600 AN: 5176

South Asian (SAS) AF: 0.286 AC: 1376 AN: 4816

European-Finnish (FIN) AF: 0.185 AC: 1954 AN: 10588

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12920 AN: 67982

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.185 Hom.: 6536

Bravo AF: 0.167

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.47
PhyloP100		0.80
PromoterAI		0.0032	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9368606; hg19: chr6-29518665;