6-29387425-G-C

Variant names:

• chr6-29387425-G-C
• rs3094548
• ENST00000377154.1:c.-82-31148C>G

Variant summary

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

The ENST00000377154.1(OR5V1):​c.-82-31148C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,874 control chromosomes in the GnomAD database, including 32,207 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 0.65 (32207 hom., cov: 31)
• Consequence: OR5V1 ENST00000377154.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 13 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377154.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR5V1	ENST00000377154.1	TSL:6	c.-82-31148C>G		intron	N/A	ENSP00000366359.1

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98093 AN: 151756 Hom.: 32172 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.646 AC: 98180 AN: 151874 Hom.: 32207 Cov.: 31 AF XY: 0.654 AC XY: 48561 AN XY: 74240

African (AFR) AF: 0.541 AC: 22379 AN: 41366

American (AMR) AF: 0.619 AC: 9451 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2141 AN: 3466

East Asian (EAS) AF: 0.654 AC: 3371 AN: 5158

South Asian (SAS) AF: 0.663 AC: 3185 AN: 4802

European-Finnish (FIN) AF: 0.822 AC: 8686 AN: 10570

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46817 AN: 67938

Other (OTH) AF: 0.640 AC: 1345 AN: 2102

Alfa AF: 0.660 Hom.: 16528

Bravo AF: 0.625

Asia WGS AF: 0.656 AC: 2281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.0
DANN	Benign	0.87
PhyloP100		-1.0
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: rs3094548; hg19: chr6-29355202;