11-5988845-T-G

Variant names:

• chr11-5988845-T-G
• rs4254056
• XM_047426926.1:c.*469-14875T>G

Variant summary

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

The XM_047426926.1(OR56A3):​c.*469-14875T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,140 control chromosomes in the GnomAD database, including 41,339 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 0.73 (41339 hom., cov: 33)
• Consequence: OR56A3 XM_047426926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR56A3	XM_047426926.1	c.*469-14875T>G		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: 0.731 AC: 111094 AN: 152020 Hom.: 41327 Cov.: 33

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.731 AC: 111149 AN: 152140 Hom.: 41339 Cov.: 33 AF XY: 0.730 AC XY: 54290 AN XY: 74368

African (AFR) AF: 0.585 AC: 24273 AN: 41476

American (AMR) AF: 0.781 AC: 11939 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2419 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4528 AN: 5182

South Asian (SAS) AF: 0.761 AC: 3675 AN: 4826

European-Finnish (FIN) AF: 0.768 AC: 8118 AN: 10576

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53771 AN: 67996

Other (OTH) AF: 0.730 AC: 1543 AN: 2114

Alfa AF: 0.773 Hom.: 25441

Bravo AF: 0.728

Asia WGS AF: 0.742 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.35
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs4254056; hg19: chr11-6010075;