rs1928623

Variant names:

• chr9-122546730-C-A
• rs1928623
• XM_017014285.2:c.*23-201G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431442.3(ENSG00000234156):​n.1362+43860C>A 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: ENSG00000234156 ENST00000431442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 2 publications found

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:):

OR1J2 (HGNC:8209): (olfactory receptor family 1 subfamily J member 2) 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 (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431442.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234156	ENST00000431442.3	TSL:3	n.1362+43860C>A		intron	N/A
	ENSG00000234156	ENST00000723589.1		n.1045-59916C>A		intron	N/A
	ENSG00000234156	ENST00000723590.1		n.498-59916C>A		intron	N/A

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

African (AFR) AF: 0.844 AC: 35038 AN: 41518

American (AMR) AF: 0.773 AC: 11810 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2714 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5163 AN: 5184

South Asian (SAS) AF: 0.809 AC: 3906 AN: 4826

European-Finnish (FIN) AF: 0.684 AC: 7217 AN: 10554

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47141 AN: 67972

Other (OTH) AF: 0.784 AC: 1652 AN: 2108

Alfa AF: 0.714 Hom.: 5112

Bravo AF: 0.772

Asia WGS AF: 0.901 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.26
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1928623; hg19: chr9-125309009;