rs4837971

Variant names:

• chr9-122487205-G-A
• rs4837971
• ENST00000431442.3:n.1187-15490G>A

Variant summary

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

The ENST00000431442.3(ENSG00000234156):​n.1187-15490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,034 control chromosomes in the GnomAD database, including 32,555 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 0.64 (32555 hom., cov: 31)
• Consequence: ENSG00000234156 ENST00000431442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 2 publications found

Genes affected

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR1J2	XM_024447516.2	c.-189-15490G>A		intron_variant	Intron 1 of 2		XP_024303284.1
OR1J2	XM_024447517.2	c.-107+11390G>A		intron_variant	Intron 2 of 3		XP_024303285.1
OR1J2	XR_007061271.1	n.1364+11390G>A		intron_variant	Intron 3 of 4
OR1J2	XR_007061274.1	n.1598-393G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234156	ENST00000431442.3	n.1187-15490G>A		intron_variant	Intron 6 of 9	3
ENSG00000234156	ENST00000723589.1	n.1044+18020G>A		intron_variant	Intron 4 of 4
ENSG00000234156	ENST00000723590.1	n.497+18020G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96732 AN: 151918 Hom.: 32492 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.637 AC: 96861 AN: 152034 Hom.: 32555 Cov.: 31 AF XY: 0.639 AC XY: 47487 AN XY: 74304

African (AFR) AF: 0.865 AC: 35893 AN: 41512

American (AMR) AF: 0.612 AC: 9348 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2685 AN: 5174

South Asian (SAS) AF: 0.647 AC: 3110 AN: 4810

European-Finnish (FIN) AF: 0.598 AC: 6312 AN: 10550

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35838 AN: 67942

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.580 Hom.: 12449

Bravo AF: 0.645

Asia WGS AF: 0.637 AC: 2215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.16
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4837971; hg19: chr9-125249484;