19-14917370-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.305 AC: 3404 AN: 11152

American (AMR) AF: 0.506 AC: 15940 AN: 31514

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 3646 AN: 12304

East Asian (EAS) AF: 0.491 AC: 11624 AN: 23696

South Asian (SAS) AF: 0.533 AC: 30013 AN: 56310

European-Finnish (FIN) AF: 0.475 AC: 17291 AN: 36422

Middle Eastern (MID) AF: 0.282 AC: 544 AN: 1932

European-Non Finnish (NFE) AF: 0.448 AC: 106050 AN: 236736

Other (OTH) AF: 0.424 AC: 8981 AN: 21162

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

African (AFR) AF: 0.314 AC: 13001 AN: 41456

American (AMR) AF: 0.452 AC: 6902 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2242 AN: 5156

South Asian (SAS) AF: 0.541 AC: 2605 AN: 4812

European-Finnish (FIN) AF: 0.472 AC: 4965 AN: 10528

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29847 AN: 67930

Other (OTH) AF: 0.369 AC: 778 AN: 2108

Alfa AF: 0.423 Hom.: 44357

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
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs1122713; hg19: chr19-15028182;