NM_001005205.3:c.-21+2121C>T

Variant names:

• chr11-56356446-C-T
• rs7940239
• NM_001005205.3:c.-21+2121C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OR8J1	NM_001005205.3	c.-21+2121C>T		intron_variant	Intron 1 of 1	ENST00000533152.3	NP_001005205.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR8J1	ENST00000533152.3	c.-21+2121C>T		intron_variant	Intron 1 of 1	6	NM_001005205.3	ENSP00000477259.3
OR8J1	ENST00000641406.1	n.35+2121C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.726 AC: 30098 AN: 41460

American (AMR) AF: 0.770 AC: 11762 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2002 AN: 3468

East Asian (EAS) AF: 0.865 AC: 4474 AN: 5174

South Asian (SAS) AF: 0.799 AC: 3850 AN: 4816

European-Finnish (FIN) AF: 0.760 AC: 8038 AN: 10572

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45022 AN: 67964

Other (OTH) AF: 0.707 AC: 1494 AN: 2112

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7940239; hg19: chr11-56123922;