rs1945245

Positions:

• chr11-56381651-C-T

Variant summary

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

The ENST00000534005.1(OR8L1P):​n.17C>T 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 0.247 in 151,904 control chromosomes in the GnomAD database, including 4,740 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 0.25 (4740 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: OR8L1P ENST00000534005.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.85

Genes affected

OR8L1P (HGNC:15316): (olfactory receptor family 8 subfamily L member 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR8L1P	ENST00000534005.1	n.17C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37544 AN: 151782 Hom.: 4739 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.247

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.247 AC: 37555 AN: 151900 Hom.: 4740 Cov.: 32 AF XY: 0.241 AC XY: 17927 AN XY: 74256

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.245

Alfa AF: 0.256 Hom.: 1052

Bravo AF: 0.249

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1945245; hg19: chr11-56149127;