11-6013029-C-T

Variant names:

• chr11-6013029-C-T
• rs10769565
• XM_047426926.1:c.*679+8518C>T

Variant summary

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

The XR_007062481.1(OR56A3):​n.354+6281C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,112 control chromosomes in the GnomAD database, including 38,079 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 0.70 (38079 hom., cov: 34)
• Consequence: OR56A3 XR_007062481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107123 AN: 151994 Hom.: 38031 Cov.: 34

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.705 AC: 107230 AN: 152112 Hom.: 38079 Cov.: 34 AF XY: 0.712 AC XY: 52924 AN XY: 74348

African (AFR) AF: 0.716 AC: 29711 AN: 41502

American (AMR) AF: 0.773 AC: 11836 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2385 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4854 AN: 5152

South Asian (SAS) AF: 0.767 AC: 3694 AN: 4816

European-Finnish (FIN) AF: 0.691 AC: 7312 AN: 10586

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45061 AN: 67964

Other (OTH) AF: 0.712 AC: 1503 AN: 2112

Alfa AF: 0.685 Hom.: 5630

Bravo AF: 0.713

Asia WGS AF: 0.877 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.62
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10769565; hg19: chr11-6034259;