rs10489854

Positions:

• chr1-159279069-C-T

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:):

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/exons	MANE	Protein	UniProt
OR10J2P		n.159279069C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR10J2P	ENST00000514684.1	n.933G>A		non_coding_transcript_exon_variant	1/1	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;