rs10489854

Variant names:

• chr1-159279069-C-T
• rs10489854
• ENST00000514684.1:n.933G>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000514684.1(OR10J2P):​n.933G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.09 in 168,166 control chromosomes in the GnomAD database, including 1,367 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 0.090 (1220 hom., cov: 32)
  • Exomes 𝑓: 0.090 (147 hom.)
• Consequence: OR10J2P ENST00000514684.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

Genes affected

OR10J2P (HGNC:14991): (olfactory receptor family 10 subfamily J member 2 pseudogene) 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR10J2P		n.159279069C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR10J2P	ENST00000514684.1	n.933G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0900 AC: 13678 AN: 152002 Hom.: 1220 Cov.: 32

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0504

Gnomad OTH AF: 0.0861

GnomAD4 exome AF: 0.0898 AC: 1441 AN: 16046 Hom.: 147 Cov.: 0 AF XY: 0.0909 AC XY: 847 AN XY: 9314

Gnomad4 AFR exome AF: 0.0534

Gnomad4 AMR exome AF: 0.110

Gnomad4 ASJ exome AF: 0.0735

Gnomad4 EAS exome AF: 0.477

Gnomad4 SAS exome AF: 0.206

Gnomad4 FIN exome AF: 0.0663

Gnomad4 NFE exome AF: 0.0452

Gnomad4 OTH exome AF: 0.0655

GnomAD4 genome AF: 0.0900 AC: 13689 AN: 152120 Hom.: 1220 Cov.: 32 AF XY: 0.0949 AC XY: 7060 AN XY: 74366

Gnomad4 AFR AF: 0.0845

Gnomad4 AMR AF: 0.0999

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0504

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0682 Hom.: 415

Bravo AF: 0.0927

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	12
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489854; hg19: chr1-159248859;