16-3327582-T-C

Position:

• chr16-3327582-T-C

Variant summary

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

The XM_047434179.1(OR2C1):​c.-44+4569T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 150,798 control chromosomes in the GnomAD database, including 4,357 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 0.23 (4357 hom., cov: 30)
• Consequence: OR2C1 XM_047434179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

Genes affected

OR2C1 (HGNC:8242): (olfactory receptor family 2 subfamily C member 1) 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2C1	XM_047434179.1	c.-44+4569T>C		intron_variant			XP_047290135.1
		n.3327582T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34360 AN: 150680 Hom.: 4340 Cov.: 30

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.196

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.228 AC: 34423 AN: 150798 Hom.: 4357 Cov.: 30 AF XY: 0.236 AC XY: 17338 AN XY: 73550

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.206

Alfa AF: 0.180 Hom.: 3685

Bravo AF: 0.219

Asia WGS AF: 0.453 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6501170; hg19: chr16-3377582;