11-5154790-T-G

Position:

• chr11-5154790-T-G

Variant summary

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

The 11-5154790-T-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,856 control chromosomes in the GnomAD database, including 17,536 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 0.48 (17535 hom., cov: 31)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: OR52A1 NM_012375.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

OR52A1 (HGNC:8318): (olfactory receptor family 52 subfamily A member 1) 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR52A1	NM_012375.3			upstream_gene_variant		ENST00000380367.3	NP_036507.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR52A1	ENST00000380367.3			upstream_gene_variant			NM_012375.3	ENSP00000369725	P1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72729 AN: 151732 Hom.: 17496 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.478

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.480 AC: 72821 AN: 151850 Hom.: 17535 Cov.: 31 AF XY: 0.478 AC XY: 35507 AN XY: 74210

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.482

Alfa AF: 0.485 Hom.: 5344

Bravo AF: 0.488

Asia WGS AF: 0.513 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4910715; hg19: chr11-5176020; COSMIC: COSV61092584;