rs734777

Variant names:

• chr11-58343636-T-G
• rs734777
• ENST00000531766.1:n.*101A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531766.1(OR5B19P):​n.*101A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,984 control chromosomes in the GnomAD database, including 2,132 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 0.16 (2132 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: OR5B19P ENST00000531766.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

OR5B19P (HGNC:15269): (olfactory receptor family 5 subfamily B member 19 pseudogene) 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 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
OR5B19P	ENST00000531766.1	n.*101A>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24175 AN: 151866 Hom.: 2128 Cov.: 32

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.159 AC: 24193 AN: 151984 Hom.: 2132 Cov.: 32 AF XY: 0.162 AC XY: 12068 AN XY: 74280

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.169

Alfa AF: 0.183 Hom.: 343

Bravo AF: 0.152

Asia WGS AF: 0.132 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.31
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs734777; hg19: chr11-58111109;