Variant 19-111079-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001005240.3(OR4F17):c.401G>A(p.Cys134Tyr) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00011 ( 0 hom., cov: 28)

Exomes 𝑓: 0.000079 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

OR4F17
NM_001005240.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.52

Variant links:

Genes affected

OR4F17 (HGNC:15381): (olfactory receptor family 4 subfamily F member 17) 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]

OR4F17 links:

OR4F17 (HGNC:):

OR4F17 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.24606088).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4F17	NM_001005240.3 linkuse as main transcript	c.401G>A	p.Cys134Tyr	missense_variant	3/3	ENST00000585993.3	NP_001005240.1	Q8NGA8A0A126GWN0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
OR4F17	ENST00000585993.3 linkuse as main transcript	c.401G>A	p.Cys134Tyr	missense_variant	3/3	6	NM_001005240.3	ENSP00000467301.1	Q8NGA8
OR4F17	ENST00000618231.3 linkuse as main transcript	c.464G>A	p.Cys155Tyr	missense_variant	2/2	6		ENSP00000493422.2	A0A2U3U062
OR4F17	ENST00000318050.4 linkuse as main transcript	c.401G>A	p.Cys134Tyr	missense_variant	1/1	6		ENSP00000315047.3	Q8NGA8
OR4F17	ENST00000641591.1 linkuse as main transcript	n.194+398G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

150342

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000243

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000333

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000148

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000280

AC:

AN:

53576

Hom.:

AF XY:

0.000297

AC XY:

AN XY:

26916

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00102

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000192

Gnomad OTH exome

AF:

0.000531

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000793

AC:

AN:

1236174

Hom.:

Cov.:

AF XY:

0.0000804

AC XY:

AN XY:

621622

show subpopulations

Gnomad4 AFR exome

AF:

0.0000653

Gnomad4 AMR exome

AF:

0.000602

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000590

Gnomad4 OTH exome

AF:

0.000286

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000106

AC:

AN:

150460

Hom.:

Cov.:

AF XY:

0.000109

AC XY:

AN XY:

73354

show subpopulations

Gnomad4 AFR

AF:

0.0000242

Gnomad4 AMR

AF:

0.000333

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000148

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000223

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 30, 2022

The c.401G>A (p.C134Y) alteration is located in exon 1 (coding exon 1) of the OR4F17 gene. This alteration results from a G to A substitution at nucleotide position 401, causing the cysteine (C) at amino acid position 134 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_addAF

Benign

-0.077

BayesDel_noAF

Benign

-0.35

CADD

Uncertain

DANN

Benign

0.93

DEOGEN2

Benign

0.028

T;.;T

Eigen

Uncertain

0.23

Eigen_PC

Benign

-0.0013

FATHMM_MKL

Benign

0.41

LIST_S2

Benign

0.57

.;T;T

M_CAP

Benign

0.0011

MetaRNN

Benign

0.25

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Pathogenic

3.3

M;.;M

PrimateAI

Uncertain

0.57

PROVEAN

Pathogenic

-9.4

.;.;D

REVEL

Benign

0.088

Sift

Uncertain

0.0070

.;.;D

Sift4G

Pathogenic

0.0

D;.;D

Polyphen

1.0

D;.;D

Vest4

0.57

MutPred

0.36

Loss of stability (P = 0.2125);.;Loss of stability (P = 0.2125);

MVP

0.64

MPC

5.0

ClinPred

0.61

GERP RS

2.5

Varity_R

0.62

gMVP

0.19

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over