rs1122713

Variant names:

• chr19-14917370-A-G
• rs1122713
• ENST00000597719.1:n.943A>G

Variant summary

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

The ENST00000597719.1(OR7A11P):​n.943A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 583,162 control chromosomes in the GnomAD database, including 59,903 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 0.41 (12882 hom., cov: 32)
  • Exomes 𝑓: 0.46 (47021 hom.)
• Consequence: OR7A11P ENST00000597719.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26

Genes affected

OR7A11P (HGNC:8357): (olfactory receptor family 7 subfamily A member 11 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR7A11P		n.14917370A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR7A11P	ENST00000597719.1	n.943A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61484 AN: 151816 Hom.: 12858 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.458 AC: 197493 AN: 431228 Hom.: 47021 Cov.: 3 AF XY: 0.461 AC XY: 110469 AN XY: 239814

Gnomad4 AFR exome AF: 0.305

Gnomad4 AMR exome AF: 0.506

Gnomad4 ASJ exome AF: 0.296

Gnomad4 EAS exome AF: 0.491

Gnomad4 SAS exome AF: 0.533

Gnomad4 FIN exome AF: 0.475

Gnomad4 NFE exome AF: 0.448

Gnomad4 OTH exome AF: 0.424

GnomAD4 genome AF: 0.405 AC: 61546 AN: 151934 Hom.: 12882 Cov.: 32 AF XY: 0.411 AC XY: 30491 AN XY: 74214

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.369

Alfa AF: 0.426 Hom.: 28718

Bravo AF: 0.396

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1122713; hg19: chr19-15028182;