rs965975

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-247758586-C-G
• chr1-247758586-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_012353.3(OR1C1):​c.-13-167G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR1C1	NM_012353.3	c.-13-167G>C		intron_variant	Intron 1 of 1	ENST00000641256.1	NP_036485.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR1C1	ENST00000641256.1	c.-13-167G>C		intron_variant	Intron 1 of 1		NM_012353.3	ENSP00000493457.1

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 413842 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 216358

African (AFR) AF: 0.00 AC: 0 AN: 11966

American (AMR) AF: 0.00 AC: 0 AN: 17890

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13022

East Asian (EAS) AF: 0.00 AC: 0 AN: 30110

South Asian (SAS) AF: 0.00 AC: 0 AN: 36996

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27034

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1854

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 250468

Other (OTH) AF: 0.00 AC: 0 AN: 24502

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.53
PhyloP100		-0.66
PromoterAI		0.0055	Neutral

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;