rs9303397

Variant names:

• chr17-58150642-C-A
• rs9303397
• NM_001386095.1:c.-127+846C>A

Variant summary

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

The NM_001386095.1(OR4D1):​c.-127+846C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,924 control chromosomes in the GnomAD database, including 25,385 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 0.57 (25385 hom., cov: 31)
• Consequence: OR4D1 NM_001386095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 11 publications found

Genes affected

OR4D1 (HGNC:8293): (olfactory receptor family 4 subfamily D 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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR4D1	NM_001386095.1	c.-127+846C>A		intron_variant	Intron 2 of 3	ENST00000268912.6	NP_001373024.1
OR4D1	NM_012374.2	c.-20+846C>A		intron_variant	Intron 2 of 2		NP_036506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR4D1	ENST00000268912.6	c.-127+846C>A		intron_variant	Intron 2 of 3	6	NM_001386095.1	ENSP00000365451.3
OR4D1	ENST00000641449.1	c.-20+846C>A		intron_variant	Intron 2 of 2			ENSP00000493234.1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86849 AN: 151808 Hom.: 25373 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.572 AC: 86897 AN: 151924 Hom.: 25385 Cov.: 31 AF XY: 0.574 AC XY: 42643 AN XY: 74266

African (AFR) AF: 0.459 AC: 19017 AN: 41418

American (AMR) AF: 0.603 AC: 9213 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2300 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4346 AN: 5164

South Asian (SAS) AF: 0.659 AC: 3176 AN: 4816

European-Finnish (FIN) AF: 0.622 AC: 6561 AN: 10542

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40119 AN: 67924

Other (OTH) AF: 0.592 AC: 1250 AN: 2110

Alfa AF: 0.592 Hom.: 116348

Bravo AF: 0.569

Asia WGS AF: 0.743 AC: 2586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.64
DANN	Benign	0.73
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs9303397; hg19: chr17-56228003;