rs7395662

Variant names:

• chr11-48497341-A-G
• rs7395662
• ENST00000527255.1:n.*61A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-48497341-A-G
• chr11-48497341-A-T

Variant summary

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

The ENST00000527255.1(OR4A46P):​n.*61A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,948 control chromosomes in the GnomAD database, including 24,795 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 0.56 (24794 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: OR4A46P ENST00000527255.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

OR4A46P (HGNC:31265): (olfactory receptor family 4 subfamily A member 46 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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
OR4A46P	ENST00000527255.1	n.*61A>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85302 AN: 151828 Hom.: 24773 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.575

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.562 AC: 85372 AN: 151946 Hom.: 24794 Cov.: 32 AF XY: 0.560 AC XY: 41604 AN XY: 74252

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.577

Alfa AF: 0.610 Hom.: 66690

Bravo AF: 0.557

Asia WGS AF: 0.432 AC: 1502 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7395662; hg19: chr11-48518893;