rs10262256

Variant names:

• chr7-143967377-C-A
• rs10262256
• ENST00000470988.1:n.146+8269C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-143967377-C-A
• chr7-143967377-C-T

Variant summary

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

The ENST00000470988.1(OR2F1):​n.146+8269C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,110 control chromosomes in the GnomAD database, including 2,251 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 0.15 (2251 hom., cov: 32)
• Consequence: OR2F1 ENST00000470988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 2 publications found

Genes affected

OR2F1 (HGNC:8246): (olfactory receptor family 2 subfamily F 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jun 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2F1	ENST00000470988.1	n.146+8269C>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23278 AN: 151990 Hom.: 2242 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.153 AC: 23340 AN: 152110 Hom.: 2251 Cov.: 32 AF XY: 0.156 AC XY: 11591 AN XY: 74374

African (AFR) AF: 0.246 AC: 10208 AN: 41474

American (AMR) AF: 0.216 AC: 3299 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3470

East Asian (EAS) AF: 0.177 AC: 913 AN: 5172

South Asian (SAS) AF: 0.124 AC: 595 AN: 4814

European-Finnish (FIN) AF: 0.150 AC: 1581 AN: 10570

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0869 AC: 5908 AN: 67998

Other (OTH) AF: 0.157 AC: 332 AN: 2116

Alfa AF: 0.119 Hom.: 662

Bravo AF: 0.167

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.30
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs10262256; hg19: chr7-143664470;