XM_047426926.1:c.*469-6308A>C

Variant names:

• chr11-5997412-A-C
• rs7947527
• XM_047426926.1:c.*469-6308A>C

Variant summary

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

The XM_047426926.1(OR56A3):​c.*469-6308A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,962 control chromosomes in the GnomAD database, including 28,960 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 0.61 (28960 hom., cov: 31)
• Consequence: OR56A3 XM_047426926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 3 publications found

Genes affected

OR56A3 (HGNC:14786): (olfactory receptor family 56 subfamily A member 3) 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR56A3	XM_047426926.1	c.*469-6308A>C		intron_variant	Intron 3 of 5		XP_047282882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92950 AN: 151842 Hom.: 28936 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.612 AC: 93030 AN: 151962 Hom.: 28960 Cov.: 31 AF XY: 0.609 AC XY: 45226 AN XY: 74266

African (AFR) AF: 0.646 AC: 26781 AN: 41444

American (AMR) AF: 0.517 AC: 7901 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2211 AN: 3468

East Asian (EAS) AF: 0.424 AC: 2186 AN: 5150

South Asian (SAS) AF: 0.785 AC: 3785 AN: 4820

European-Finnish (FIN) AF: 0.545 AC: 5750 AN: 10550

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42378 AN: 67948

Other (OTH) AF: 0.614 AC: 1293 AN: 2106

Alfa AF: 0.627 Hom.: 17381

Bravo AF: 0.605

Asia WGS AF: 0.651 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7947527; hg19: chr11-6018642;