rs9368606

Positions:

• chr6-29550888-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001396058.1(OR2I1P):​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: OR2I1P NM_001396058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798

Genes affected

OR2I1P (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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2I1P	NM_001396058.1	c.6+31A>C		intron_variant		ENST00000641137.2	NP_001382987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2I1P	ENST00000641137.2	c.6+31A>C		intron_variant			NM_001396058.1	ENSP00000493715	P1
OR2I1P	ENST00000641730.1	n.451+31A>C		intron_variant, non_coding_transcript_variant
OR2I1P	ENST00000642037.1	n.194+288A>C		intron_variant, non_coding_transcript_variant

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

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

Gnomad4 AFR AF: 0.0692

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.168

Alfa AF: 0.187 Hom.: 1260

Bravo AF: 0.167

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9368606; hg19: chr6-29518665;