rs1122713

Positions:

• chr19-14917370-A-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:):

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/exons	MANE	Protein	UniProt
OR7A11P		n.14917370A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR7A11P	ENST00000597719.1	n.943A>G		non_coding_transcript_exon_variant	1/1	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;