rs7772982

Variant names:

• chr6-29373230-T-C
• rs7772982
• ENST00000377154.1:c.-82-16953A>G

Variant summary

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

The ENST00000377154.1(OR5V1):​c.-82-16953A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,878 control chromosomes in the GnomAD database, including 3,873 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 0.22 (3873 hom., cov: 32)
• Consequence: OR5V1 ENST00000377154.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 12 publications found

Genes affected

OR5V1 (HGNC:13972): (olfactory receptor family 5 subfamily V 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]

OR12D3 (HGNC:13963): (olfactory receptor family 12 subfamily D member 3) 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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR12D3	NM_030959.3	c.*1107A>G		downstream_gene_variant		ENST00000396806.3	NP_112221.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR5V1	ENST00000377154.1	c.-82-16953A>G		intron_variant	Intron 3 of 3	6		ENSP00000366359.1
OR12D3	ENST00000396806.3	c.*1107A>G		downstream_gene_variant		6	NM_030959.3	ENSP00000380023.3

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33805 AN: 151760 Hom.: 3867 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.223 AC: 33830 AN: 151878 Hom.: 3873 Cov.: 32 AF XY: 0.224 AC XY: 16652 AN XY: 74220

African (AFR) AF: 0.275 AC: 11376 AN: 41426

American (AMR) AF: 0.222 AC: 3393 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3462

East Asian (EAS) AF: 0.241 AC: 1251 AN: 5184

South Asian (SAS) AF: 0.235 AC: 1135 AN: 4822

European-Finnish (FIN) AF: 0.202 AC: 2129 AN: 10518

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12784 AN: 67886

Other (OTH) AF: 0.231 AC: 487 AN: 2106

Alfa AF: 0.202 Hom.: 10472

Bravo AF: 0.230

Asia WGS AF: 0.248 AC: 859 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.1
DANN	Benign	0.75
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7772982; hg19: chr6-29341007; COSMIC: COSV65828398; COSMIC: COSV65828398;