6-29371185-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.42
Variant links:
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]

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ACMG classification

Classification made for transcript

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 Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OR5V1ENST00000377154.1 linkuse as main transcriptc.-82-14908C>T intron_variant ENSP00000366359 P1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4713213; hg19: chr6-29338962; API