rs1928623

Positions:

• chr9-122546730-C-A
• chr9-122546730-C-G
• chr9-122546730-C-T

Variant summary

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

The XM_017014285.2(OR1L8):​c.*23-201G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,120 control chromosomes in the GnomAD database, including 44,509 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 0.76 (44509 hom., cov: 33)
• Consequence: OR1L8 XM_017014285.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

OR1L8 (HGNC:15110): (olfactory receptor family 1 subfamily L member 8) 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]

ENSG00000234156 (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 (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1L8	XM_017014285.2	c.*23-201G>T		intron_variant			XP_016869774.1
OR1J2	XR_007061271.1	n.1541-33223C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234156	ENST00000431442.2	n.1362+43860C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115486 AN: 152002 Hom.: 44463 Cov.: 33

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.782

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.760 AC: 115587 AN: 152120 Hom.: 44509 Cov.: 33 AF XY: 0.762 AC XY: 56613 AN XY: 74342

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.784

Alfa AF: 0.709 Hom.: 4833

Bravo AF: 0.772

Asia WGS AF: 0.901 AC: 3130 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	1.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928623; hg19: chr9-125309009;