rs2878329

Variant names:

• chr19-9215066-C-T
• rs2878329
• NM_001005191.3:c.-13-216G>A

Variant summary

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

The NM_001005191.3(OR7D4):​c.-13-216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,908 control chromosomes in the GnomAD database, including 2,136 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 0.14 (2136 hom., cov: 31)
• Consequence: OR7D4 NM_001005191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 5 publications found

Genes affected

OR7D4 (HGNC:8380): (olfactory receptor family 7 subfamily D member 4) 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]

OR7E24 (HGNC:8396): (olfactory receptor family 7 subfamily E member 24) 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR7D4	NM_001005191.3	c.-13-216G>A		intron_variant	Intron 1 of 1	ENST00000641669.1	NP_001005191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR7D4	ENST00000641669.1	c.-13-216G>A		intron_variant	Intron 1 of 1		NM_001005191.3	ENSP00000493383.1
OR7D4	ENST00000641244.1	c.-16-213G>A		intron_variant	Intron 1 of 1			ENSP00000493404.1
OR7D4	ENST00000308682.3	c.-229G>A		upstream_gene_variant		6		ENSP00000310488.2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20574 AN: 151790 Hom.: 2131 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0490

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.136 AC: 20601 AN: 151908 Hom.: 2136 Cov.: 31 AF XY: 0.135 AC XY: 10009 AN XY: 74274

African (AFR) AF: 0.275 AC: 11375 AN: 41404

American (AMR) AF: 0.125 AC: 1910 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.0491 AC: 253 AN: 5152

South Asian (SAS) AF: 0.204 AC: 984 AN: 4824

European-Finnish (FIN) AF: 0.0271 AC: 286 AN: 10536

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0742 AC: 5045 AN: 67948

Other (OTH) AF: 0.132 AC: 277 AN: 2106

Alfa AF: 0.103 Hom.: 1713

Bravo AF: 0.148

Asia WGS AF: 0.125 AC: 436 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	6.0
DANN	Benign	0.42
PhyloP100		-1.5
PromoterAI		0.011	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2878329; hg19: chr19-9325742;