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. The variant received -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
• Publications: 57 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.431 AC: 17880 AN: 41458

American (AMR) AF: 0.611 AC: 9319 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2144 AN: 3472

East Asian (EAS) AF: 0.458 AC: 2355 AN: 5140

South Asian (SAS) AF: 0.420 AC: 2023 AN: 4822

European-Finnish (FIN) AF: 0.673 AC: 7089 AN: 10536

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42473 AN: 67954

Other (OTH) AF: 0.577 AC: 1218 AN: 2110

Alfa AF: 0.603 Hom.: 127944

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7395662; hg19: chr11-48518893;