rs11227638

Variant names:

• chr11-56252109-A-T
• rs11227638
• NM_001004747.2:c.-145A>T

Variant summary

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

The NM_001004747.2(OR5T3):​c.-145A>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 652,830 control chromosomes in the GnomAD database, including 5,018 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 0.11 (1002 hom., cov: 32)
  • Exomes 𝑓: 0.12 (4016 hom.)
• Consequence: OR5T3 NM_001004747.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 3 publications found

Genes affected

OR5T3 (HGNC:15297): (olfactory receptor family 5 subfamily T 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR5T3	NM_001004747.2	c.-145A>T		upstream_gene_variant		ENST00000313033.4	NP_001004747.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR5T3	ENST00000313033.4	c.-145A>T		upstream_gene_variant		6	NM_001004747.2	ENSP00000323612.3

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15984 AN: 151906 Hom.: 1003 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0869

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0856

GnomAD4 exome AF: 0.121 AC: 60417 AN: 500806 Hom.: 4016 AF XY: 0.121 AC XY: 31203 AN XY: 258180

African (AFR) AF: 0.0577 AC: 748 AN: 12958

American (AMR) AF: 0.104 AC: 1588 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0835 AC: 1084 AN: 12982

East Asian (EAS) AF: 0.129 AC: 3920 AN: 30400

South Asian (SAS) AF: 0.123 AC: 3807 AN: 31042

European-Finnish (FIN) AF: 0.178 AC: 6290 AN: 35378

Middle Eastern (MID) AF: 0.0800 AC: 165 AN: 2062

European-Non Finnish (NFE) AF: 0.119 AC: 39889 AN: 333900

Other (OTH) AF: 0.109 AC: 2926 AN: 26862

GnomAD4 genome AF: 0.105 AC: 15978 AN: 152024 Hom.: 1002 Cov.: 32 AF XY: 0.109 AC XY: 8077 AN XY: 74320

African (AFR) AF: 0.0578 AC: 2401 AN: 41526

American (AMR) AF: 0.0927 AC: 1413 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0869 AC: 301 AN: 3464

East Asian (EAS) AF: 0.141 AC: 728 AN: 5172

South Asian (SAS) AF: 0.121 AC: 583 AN: 4828

European-Finnish (FIN) AF: 0.199 AC: 2104 AN: 10562

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8141 AN: 67908

Other (OTH) AF: 0.0838 AC: 177 AN: 2112

Alfa AF: 0.109 Hom.: 133

Bravo AF: 0.0963

Asia WGS AF: 0.108 AC: 374 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.34
PhyloP100		-0.43
PromoterAI		0.0034	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11227638; hg19: chr11-56019585;