chr6-29304235-C-T

Variant names:

• chr6-29304235-C-T
• rs3117426
• NM_030946.2:c.-28-2427C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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]

ENSG00000295863 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030946.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR14J1	NM_030946.2	MANE Select	c.-28-2427C>T		intron	N/A	NP_112208.1	Q9UGF5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR14J1	ENST00000641895.1	MANE Select	c.-28-2427C>T		intron	N/A	ENSP00000492893.1	Q9UGF5
	ENSG00000295863	ENST00000733278.1		n.246-13683G>A		intron	N/A
	ENSG00000295863	ENST00000733279.1		n.390-13683G>A		intron	N/A

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

African (AFR) AF: 0.267 AC: 11063 AN: 41446

American (AMR) AF: 0.165 AC: 2515 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3468

East Asian (EAS) AF: 0.0885 AC: 458 AN: 5176

South Asian (SAS) AF: 0.102 AC: 494 AN: 4826

European-Finnish (FIN) AF: 0.162 AC: 1710 AN: 10542

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13279 AN: 67978

Other (OTH) AF: 0.181 AC: 381 AN: 2106

Alfa AF: 0.201 Hom.: 10176

Bravo AF: 0.209

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs3117426; hg19: chr6-29272012;