chr16-3328977-T-C

Variant names:

• chr16-3328977-T-C
• rs250470
• XM_047434179.1:c.-44+5964T>C

Variant summary

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

The XM_047434179.1(OR2C1):​c.-44+5964T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 150,694 control chromosomes in the GnomAD database, including 39,890 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 0.73 (39890 hom., cov: 28)
• Consequence: OR2C1 XM_047434179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 3 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2C1	XM_047434179.1	c.-44+5964T>C		intron_variant	Intron 1 of 1		XP_047290135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.727 AC: 109464 AN: 150576 Hom.: 39886 Cov.: 28

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.727 AC: 109503 AN: 150694 Hom.: 39890 Cov.: 28 AF XY: 0.731 AC XY: 53790 AN XY: 73544

African (AFR) AF: 0.643 AC: 26183 AN: 40748

American (AMR) AF: 0.731 AC: 11011 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2578 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3312 AN: 5042

South Asian (SAS) AF: 0.836 AC: 4008 AN: 4796

European-Finnish (FIN) AF: 0.792 AC: 8260 AN: 10426

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51724 AN: 67874

Other (OTH) AF: 0.711 AC: 1481 AN: 2084

Alfa AF: 0.693 Hom.: 2127

Bravo AF: 0.712

Asia WGS AF: 0.702 AC: 2441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.83
DANN	Benign	0.64
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs250470; hg19: chr16-3378977;