rs4128725

Variant names:

• chr1-159436169-T-C
• rs4128725
• ENST00000431862.1:n.227+32673A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-159436169-T-C
• chr1-159436169-T-G

Variant summary

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

The NM_001363557.2(OR10J1):​c.-16-3607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,048 control chromosomes in the GnomAD database, including 1,142 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 0.11 (1142 hom., cov: 31)
• Consequence: OR10J1 NM_001363557.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

Genes affected

ENSG00000228560 (HGNC:):

OR10J1 (HGNC:8175): (olfactory receptor family 10 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR10J1	NM_001363557.2	c.-16-3607T>C		intron_variant	Intron 4 of 4		NP_001350486.1
OR10J1	NM_001363558.2	c.-16-3607T>C		intron_variant	Intron 3 of 3		NP_001350487.1
OR10J1	XM_047417793.1	c.-16-3607T>C		intron_variant	Intron 1 of 1		XP_047273749.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228560	ENST00000431862.1	n.227+32673A>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16430 AN: 151932 Hom.: 1142 Cov.: 31

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.108 AC: 16428 AN: 152048 Hom.: 1142 Cov.: 31 AF XY: 0.110 AC XY: 8213 AN XY: 74330

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.115

Alfa AF: 0.112 Hom.: 1285

Bravo AF: 0.114

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128725; hg19: chr1-159405959;