1-247526230-C-T

Variant names:

• chr1-247526230-C-T
• rs1881797
• NM_198074.6:c.*5319G>A

Variant summary

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

The NM_198074.6(OR2C3):​c.*5319G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,222 control chromosomes in the GnomAD database, including 42,599 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 (42599 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR2C3 NM_198074.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 23 publications found

Genes affected

OR2C3 (HGNC:15005): (olfactory receptor family 2 subfamily C member 3) 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]

GCSAML (HGNC:29583): (germinal center associated signaling and motility like) This gene encodes a protein thought to be a signaling molecule associated with germinal centers, the sites of proliferation and differentiation of mature B lymphocytes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

GCSAML-AS1 (HGNC:41244): (GCSAML antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2C3	NM_198074.6	c.*5319G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000641802.1	NP_932340.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2C3	ENST00000641802.1	c.*5319G>A		3_prime_UTR_variant	Exon 3 of 3		NM_198074.6	ENSP00000493385.1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111424 AN: 152104 Hom.: 42582 Cov.: 33

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.761

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.732 AC: 111472 AN: 152222 Hom.: 42599 Cov.: 33 AF XY: 0.737 AC XY: 54882 AN XY: 74424

African (AFR) AF: 0.496 AC: 20590 AN: 41498

American (AMR) AF: 0.760 AC: 11613 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2804 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5038 AN: 5180

South Asian (SAS) AF: 0.919 AC: 4441 AN: 4830

European-Finnish (FIN) AF: 0.797 AC: 8452 AN: 10610

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55848 AN: 68028

Other (OTH) AF: 0.764 AC: 1610 AN: 2108

Alfa AF: 0.798 Hom.: 210589

Bravo AF: 0.719

Asia WGS AF: 0.900 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.80
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1881797; hg19: chr1-247689532;