rs11724

Positions:

• chr6-29553542-C-G
• chr6-29553542-C-T

Variant summary

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

The NM_001396058.1(OR2I1P):​c.324C>G​(p.Ser108Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 398,340 control chromosomes in the GnomAD database, including 69,502 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 0.62 (29608 hom., cov: 36)
  • Exomes 𝑓: 0.57 (39894 hom.)
• Consequence: OR2I1P NM_001396058.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -13.3

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]

OR2I1P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP7: Synonymous conserved (PhyloP=-13.3 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2I1P	NM_001396058.1	c.324C>G	p.Ser108Ser	synonymous_variant	2/2	ENST00000641137.2	NP_001382987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2I1P	ENST00000641137.2	c.324C>G	p.Ser108Ser	synonymous_variant	2/2		NM_001396058.1	ENSP00000493715.1
OR2I1P	ENST00000641730.1	n.1186C>G		non_coding_transcript_exon_variant	2/2
OR2I1P	ENST00000642037.1	n.512C>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93737 AN: 152092 Hom.: 29560 Cov.: 36

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.619

GnomAD4 exome AF: 0.565 AC: 139064 AN: 246130 Hom.: 39894 Cov.: 0 AF XY: 0.561 AC XY: 70055 AN XY: 124792

Gnomad4 AFR exome AF: 0.742

Gnomad4 AMR exome AF: 0.592

Gnomad4 ASJ exome AF: 0.493

Gnomad4 EAS exome AF: 0.696

Gnomad4 SAS exome AF: 0.800

Gnomad4 FIN exome AF: 0.618

Gnomad4 NFE exome AF: 0.527

Gnomad4 OTH exome AF: 0.581

GnomAD4 genome AF: 0.617 AC: 93840 AN: 152210 Hom.: 29608 Cov.: 36 AF XY: 0.623 AC XY: 46345 AN XY: 74414

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.624

Alfa AF: 0.564 Hom.: 3062

Bravo AF: 0.621

Asia WGS AF: 0.786 AC: 2729 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11724; hg19: chr6-29521319;