rs1476203

Variant names:

• chr11-123944046-A-G
• rs1476203
• NM_001005187.1:c.-208T>C

Variant summary

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

The NM_001005187.1(OR6T1):​c.-208T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,186 control chromosomes in the GnomAD database, including 44,980 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 0.77 (44980 hom., cov: 33)
• Consequence: OR6T1 NM_001005187.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 2 publications found

Genes affected

OR6T1 (HGNC:14848): (olfactory receptor family 6 subfamily T 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR6T1	NM_001005187.1	c.-208T>C		upstream_gene_variant		ENST00000321252.3	NP_001005187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR6T1	ENST00000321252.3	c.-208T>C		upstream_gene_variant		6	NM_001005187.1	ENSP00000325203.2

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116769 AN: 152068 Hom.: 44953 Cov.: 33

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.768 AC: 116844 AN: 152186 Hom.: 44980 Cov.: 33 AF XY: 0.764 AC XY: 56857 AN XY: 74400

African (AFR) AF: 0.772 AC: 32048 AN: 41524

American (AMR) AF: 0.724 AC: 11073 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2845 AN: 3472

East Asian (EAS) AF: 0.641 AC: 3314 AN: 5174

South Asian (SAS) AF: 0.670 AC: 3229 AN: 4820

European-Finnish (FIN) AF: 0.797 AC: 8440 AN: 10586

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53296 AN: 67994

Other (OTH) AF: 0.760 AC: 1609 AN: 2116

Alfa AF: 0.792 Hom.: 110088

Bravo AF: 0.765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.60
PhyloP100		0.17
PromoterAI		0.0098	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1476203; hg19: chr11-123814753;