1-247758586-C-T

Variant names:

• chr1-247758586-C-T
• rs965975
• NM_012353.3:c.-13-167G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012353.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR1C1	NM_012353.3	MANE Select	c.-13-167G>A		intron	N/A	NP_036485.2	A0A126GV94

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR1C1	ENST00000641256.1	MANE Select	c.-13-167G>A		intron	N/A	ENSP00000493457.1	Q15619
	OR1C1	ENST00000408896.4	TSL:6	c.-180G>A		5_prime_UTR	Exon 1 of 1	ENSP00000386138.2	Q15619
	ENSG00000235749	ENST00000662798.1		n.1080+639C>T		intron	N/A

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

African (AFR) AF: 0.795 AC: 9509 AN: 11964

American (AMR) AF: 0.981 AC: 17546 AN: 17890

Ashkenazi Jewish (ASJ) AF: 0.949 AC: 12356 AN: 13018

East Asian (EAS) AF: 0.975 AC: 29337 AN: 30100

South Asian (SAS) AF: 0.952 AC: 35183 AN: 36966

European-Finnish (FIN) AF: 1.00 AC: 27033 AN: 27034

Middle Eastern (MID) AF: 0.978 AC: 1814 AN: 1854

European-Non Finnish (NFE) AF: 0.998 AC: 249850 AN: 250462

Other (OTH) AF: 0.972 AC: 23806 AN: 24500

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

African (AFR) AF: 0.799 AC: 33066 AN: 41374

American (AMR) AF: 0.969 AC: 14802 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3288 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5073 AN: 5138

South Asian (SAS) AF: 0.953 AC: 4568 AN: 4792

European-Finnish (FIN) AF: 1.00 AC: 10590 AN: 10590

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67817 AN: 68014

Other (OTH) AF: 0.952 AC: 2010 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.63
PhyloP100		-0.66
PromoterAI		-0.013	Neutral
Mutation Taster		=298/2	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs965975; hg19: chr1-247921888;