1-247758586-C-T

Position:

• chr1-247758586-C-T

Variant summary

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

The NM_012353.3(OR1C1):​c.-13-167G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 565,756 control chromosomes in the GnomAD database, including 267,190 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 0.94 (67260 hom., cov: 28)
  • Exomes 𝑓: 0.98 (199930 hom.)
• Consequence: OR1C1 NM_012353.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

OR1C1 (HGNC:8182): (olfactory receptor family 1 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]

ENSG00000235749 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1C1	NM_012353.3	c.-13-167G>A		intron_variant		ENST00000641256.1	NP_036485.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR1C1	ENST00000641256.1	c.-13-167G>A		intron_variant			NM_012353.3	ENSP00000493457.1
OR1C1	ENST00000408896.4	c.-180G>A		5_prime_UTR_variant	1/1	6		ENSP00000386138.2
ENSG00000235749	ENST00000662798.1	n.1080+639C>T		intron_variant
ENSG00000235749	ENST00000663177.1	n.463+639C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142296 AN: 151850 Hom.: 67216 Cov.: 28

Gnomad AFR AF: 0.799

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.969

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.953

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.951

GnomAD4 exome AF: 0.982 AC: 406434 AN: 413788 Hom.: 199930 Cov.: 3 AF XY: 0.981 AC XY: 212286 AN XY: 216320

Gnomad4 AFR exome AF: 0.795

Gnomad4 AMR exome AF: 0.981

Gnomad4 ASJ exome AF: 0.949

Gnomad4 EAS exome AF: 0.975

Gnomad4 SAS exome AF: 0.952

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.998

Gnomad4 OTH exome AF: 0.972

GnomAD4 genome AF: 0.937 AC: 142394 AN: 151968 Hom.: 67260 Cov.: 28 AF XY: 0.938 AC XY: 69685 AN XY: 74258

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.969

Gnomad4 ASJ AF: 0.947

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.997

Gnomad4 OTH AF: 0.952

Alfa AF: 0.956 Hom.: 11451

Bravo AF: 0.929

Asia WGS AF: 0.962 AC: 3345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs965975; hg19: chr1-247921888;