6-29384007-G-A

Variant names:

• chr6-29384007-G-A
• rs9378134
• ENST00000377154.1:c.-82-27730C>T

Variant summary

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

The ENST00000377154.1(OR5V1):​c.-82-27730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,062 control chromosomes in the GnomAD database, including 767 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 0.081 (767 hom., cov: 32)
• Consequence: OR5V1 ENST00000377154.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 4 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR5V1	ENST00000377154.1	c.-82-27730C>T		intron_variant	Intron 3 of 3	6		ENSP00000366359.1

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12285 AN: 151944 Hom.: 765 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0662

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0809 AC: 12301 AN: 152062 Hom.: 767 Cov.: 32 AF XY: 0.0809 AC XY: 6008 AN XY: 74296

African (AFR) AF: 0.157 AC: 6500 AN: 41496

American (AMR) AF: 0.0660 AC: 1009 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1070 AN: 5186

South Asian (SAS) AF: 0.0654 AC: 315 AN: 4814

European-Finnish (FIN) AF: 0.0298 AC: 315 AN: 10562

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0392 AC: 2661 AN: 67936

Other (OTH) AF: 0.0748 AC: 158 AN: 2112

Alfa AF: 0.0614 Hom.: 518

Bravo AF: 0.0887

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-1.7
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: rs9378134; hg19: chr6-29351784;