rs7940239

chr11-56356446-C-T

Variant summary

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

The NM_001005205.3(OR8J1):c.-21+2121C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,052 control chromosomes in the GnomAD database, including 38,250 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 0.71 (38250 hom., cov: 33)
• Consequence: OR8J1 NM_001005205.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

OR8J1 (HGNC:14855): (olfactory receptor family 8 subfamily J member 1) 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR8J1	NM_001005205.3	c.-21+2121C>T		intron_variant		ENST00000533152.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR8J1	ENST00000533152.3	c.-21+2121C>T		intron_variant			NM_001005205.3	P1
OR8J1	ENST00000641406.1	n.35+2121C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107293 AN: 151930 Hom.: 38196 Cov.: 33

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.706 AC: 107404 AN: 152052 Hom.: 38250 Cov.: 33 AF XY: 0.714 AC XY: 53098 AN XY: 74326

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.707

Alfa AF: 0.678 Hom.: 4839

Bravo AF: 0.706

Asia WGS AF: 0.839 AC: 2915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.77
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7940239; hg19: chr11-56123922;