rs4713213

Positions:

• chr6-29371185-G-A
• chr6-29371185-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000377154.1(OR5V1):​c.-82-14908C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,846 control chromosomes in the GnomAD database, including 18,280 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 0.48 (18280 hom., cov: 31)
• Consequence: OR5V1 ENST00000377154.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR5V1	ENST00000377154.1	c.-82-14908C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72371 AN: 151730 Hom.: 18274 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.477 AC: 72395 AN: 151846 Hom.: 18280 Cov.: 31 AF XY: 0.483 AC XY: 35826 AN XY: 74232

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.469

Alfa AF: 0.466 Hom.: 3544

Bravo AF: 0.447

Asia WGS AF: 0.529 AC: 1835 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713213; hg19: chr6-29338962;