rs3117426

Positions:

• chr6-29304235-C-T

Variant summary

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

The NM_030946.2(OR14J1):​c.-28-2427C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,012 control chromosomes in the GnomAD database, including 3,298 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 0.20 (3298 hom., cov: 32)
• Consequence: OR14J1 NM_030946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

OR14J1 (HGNC:13971): (olfactory receptor family 14 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]

LOC105375005 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR14J1	NM_030946.2	c.-28-2427C>T		intron_variant		ENST00000641895.1
LOC105375005	XR_926670.1	n.220-19275G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR14J1	ENST00000641895.1	c.-28-2427C>T		intron_variant			NM_030946.2	P1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30574 AN: 151892 Hom.: 3288 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.201 AC: 30627 AN: 152012 Hom.: 3298 Cov.: 32 AF XY: 0.194 AC XY: 14422 AN XY: 74294

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0885

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.181

Alfa AF: 0.193 Hom.: 3139

Bravo AF: 0.209

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117426; hg19: chr6-29272012;