rs17184255

chr6-29553512-C-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001396058.1(OR2I1P):c.294C>G(p.Ala98=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 398,620 control chromosomes in the GnomAD database, including 5,838 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 0.16 (4405 hom., cov: 34)
  • Exomes 𝑓: 0.063 (1433 hom.)
• Consequence: OR2I1P NM_001396058.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.60

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP7: Synonymous conserved (PhyloP=-4.6 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2I1P	NM_001396058.1	c.294C>G	p.Ala98=	synonymous_variant	2/2	ENST00000641137.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2I1P	ENST00000641137.2	c.294C>G	p.Ala98=	synonymous_variant	2/2		NM_001396058.1	P1
OR2I1P	ENST00000641730.1	n.1156C>G		non_coding_transcript_exon_variant	2/2
OR2I1P	ENST00000642037.1	n.482C>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23939 AN: 152204 Hom.: 4373 Cov.: 34

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.0627 AC: 15433 AN: 246298 Hom.: 1433 Cov.: 0 AF XY: 0.0595 AC XY: 7429 AN XY: 124904

Gnomad4 AFR exome AF: 0.449

Gnomad4 AMR exome AF: 0.0980

Gnomad4 ASJ exome AF: 0.0896

Gnomad4 EAS exome AF: 0.185

Gnomad4 SAS exome AF: 0.150

Gnomad4 FIN exome AF: 0.00892

Gnomad4 NFE exome AF: 0.0265

Gnomad4 OTH exome AF: 0.0905

GnomAD4 genome AF: 0.158 AC: 24016 AN: 152322 Hom.: 4405 Cov.: 34 AF XY: 0.156 AC XY: 11614 AN XY: 74482

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.00960

Gnomad4 NFE AF: 0.0250

Gnomad4 OTH AF: 0.157

Alfa AF: 0.102 Hom.: 361

Bravo AF: 0.181

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17184255; hg19: chr6-29521289; COSMIC: COSV63541279; COSMIC: COSV63541279;