rs9257843

chr6-29400888-T-Cchr6-29400888-T-G

Variant summary

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

The ENST00000377154.1(OR5V1):c.-83+21719A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,826 control chromosomes in the GnomAD database, including 13,187 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 0.41 (13187 hom., cov: 30)
• Consequence: OR5V1 ENST00000377154.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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.-83+21719A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62640 AN: 151708 Hom.: 13175 Cov.: 30

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.413 AC: 62669 AN: 151826 Hom.: 13187 Cov.: 30 AF XY: 0.412 AC XY: 30589 AN XY: 74188

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.421

Alfa AF: 0.426 Hom.: 9599

Bravo AF: 0.411

Asia WGS AF: 0.297 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.26

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: rs9257843; hg19: chr6-29368665;