chr17-3117358-T-C

Variant names:

• chr17-3117358-T-C
• rs2001009
• ENST00000575608.2:n.932T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000575608.2(OR1E3):​n.932T>C 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 0.141 in 300,416 control chromosomes in the GnomAD database, including 6,402 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 0.19 (5262 hom., cov: 32)
  • Exomes 𝑓: 0.088 (1140 hom.)
• Consequence: OR1E3 ENST00000575608.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618
• Publications: 1 publications found

Genes affected

OR1E3 (HGNC:8191): (olfactory receptor family 1 subfamily E member 3 (gene/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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000575608.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR1E3	ENST00000575608.2	TSL:6	n.932T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29138 AN: 152064 Hom.: 5228 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.154

GnomAD4 exome AF: 0.0884 AC: 13097 AN: 148234 Hom.: 1140 Cov.: 0 AF XY: 0.0840 AC XY: 7279 AN XY: 86646

African (AFR) AF: 0.466 AC: 1466 AN: 3144

American (AMR) AF: 0.262 AC: 2722 AN: 10398

Ashkenazi Jewish (ASJ) AF: 0.0567 AC: 159 AN: 2804

East Asian (EAS) AF: 0.0332 AC: 223 AN: 6722

South Asian (SAS) AF: 0.0563 AC: 1182 AN: 20996

European-Finnish (FIN) AF: 0.0545 AC: 525 AN: 9628

Middle Eastern (MID) AF: 0.0618 AC: 31 AN: 502

European-Non Finnish (NFE) AF: 0.0705 AC: 6117 AN: 86726

Other (OTH) AF: 0.0919 AC: 672 AN: 7314

GnomAD4 genome AF: 0.192 AC: 29236 AN: 152182 Hom.: 5262 Cov.: 32 AF XY: 0.189 AC XY: 14072 AN XY: 74430

African (AFR) AF: 0.469 AC: 19451 AN: 41458

American (AMR) AF: 0.216 AC: 3300 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0567 AC: 197 AN: 3472

East Asian (EAS) AF: 0.0374 AC: 194 AN: 5186

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4820

European-Finnish (FIN) AF: 0.0586 AC: 622 AN: 10618

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4781 AN: 68014

Other (OTH) AF: 0.154 AC: 326 AN: 2114

Alfa AF: 0.115 Hom.: 580

Bravo AF: 0.217

Asia WGS AF: 0.0930 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.57
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2001009; hg19: chr17-3020652;