Variant rs55871516 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001004734.3(OR14I1):c.647A>G(p.Tyr216Cys) variant causes a missense change. The variant allele was found at a frequency of 0.133 in 780,800 control chromosomes in the GnomAD database, including 7,455 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.14 ( 1473 hom., cov: 31)

Exomes 𝑓: 0.13 ( 5982 hom. )

Consequence

OR14I1
NM_001004734.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.08

Variant links:

Genes affected

OR14I1 (HGNC:19575): (olfactory receptor family 14 subfamily I 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]

OR14I1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017676651).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR14I1	NM_001004734.3 linkuse as main transcript	c.647A>G	p.Tyr216Cys	missense_variant	5/5		NP_001004734.1
OR14I1	XM_047420643.1 linkuse as main transcript	c.647A>G	p.Tyr216Cys	missense_variant	3/3		XP_047276599.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR14I1	ENST00000342623.5 linkuse as main transcript	c.647A>G	p.Tyr216Cys	missense_variant	1/1			ENSP00000339726	P1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20712

AN:

151914

Hom.:

1473

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.0990

GnomAD3 exomes

AF:

0.140

AC:

35229

AN:

251432

Hom.:

2645

AF XY:

0.139

AC XY:

18866

AN XY:

135888

show subpopulations

Gnomad AFR exome

AF:

0.163

Gnomad AMR exome

AF:

0.153

Gnomad ASJ exome

AF:

0.115

Gnomad EAS exome

AF:

0.170

Gnomad SAS exome

AF:

0.146

Gnomad FIN exome

AF:

0.182

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.121

GnomAD4 exome

AF:

0.133

AC:

83410

AN:

628768

Hom.:

5982

Cov.:

AF XY:

0.132

AC XY:

45343

AN XY:

342528

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.146

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.178

Gnomad4 NFE exome

AF:

0.120

Gnomad4 OTH exome

AF:

0.119

GnomAD4 genome

AF:

0.136

AC:

20720

AN:

152032

Hom.:

1473

Cov.:

AF XY:

0.139

AC XY:

10358

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.160

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.122

Gnomad4 EAS

AF:

0.161

Gnomad4 SAS

AF:

0.147

Gnomad4 FIN

AF:

0.191

Gnomad4 NFE

AF:

0.120

Gnomad4 OTH

AF:

0.0975

Alfa

AF:

0.122

Hom.:

1774

Bravo

AF:

0.131

TwinsUK

AF:

0.115

AC:

428

ALSPAC

AF:

0.113

AC:

436

ESP6500AA

AF:

0.153

AC:

674

ESP6500EA

AF:

0.115

AC:

992

ExAC

AF:

0.139

AC:

16925

Asia WGS

AF:

0.158

AC:

549

AN:

3478

EpiCase

AF:

0.109

EpiControl

AF:

0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.043

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.24

FATHMM_MKL

Uncertain

0.76

LIST_S2

Benign

0.56

MetaRNN

Benign

0.0018

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

3.7

MutationTaster

Benign

0.29

PrimateAI

Benign

0.28

PROVEAN

Pathogenic

-8.7

REVEL

Benign

0.13

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.16

MPC

0.25

ClinPred

0.070

GERP RS

3.5

Varity_R

0.83

gMVP

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over