Variant rs10838851 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001004726.1(OR4X1):c.819T>A(p.Tyr273*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,613,266 control chromosomes in the GnomAD database, including 435,620 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.69 ( 36959 hom., cov: 33)

Exomes 𝑓: 0.73 ( 398661 hom. )

Consequence

OR4X1
NM_001004726.1 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25

Variant links:

Genes affected

OR4X1 (HGNC:14854): (olfactory receptor family 4 subfamily X 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jul 2015]

OR4X1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4X1	NM_001004726.1 linkuse as main transcript	c.819T>A	p.Tyr273*	stop_gained	1/1	ENST00000320048.1	NP_001004726.1	Q8NH49

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4X1	ENST00000320048.1 linkuse as main transcript	c.819T>A	p.Tyr273*	stop_gained	1/1	6	NM_001004726.1	ENSP00000321506.1		Q8NH49

Frequencies

GnomAD3 genomes

AF:

0.690

AC:

104863

AN:

152022

Hom.:

36946

Cov.:

show subpopulations

Gnomad AFR

AF:

0.559

Gnomad AMI

AF:

0.836

Gnomad AMR

AF:

0.737

Gnomad ASJ

AF:

0.693

Gnomad EAS

AF:

0.577

Gnomad SAS

AF:

0.544

Gnomad FIN

AF:

0.811

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.757

Gnomad OTH

AF:

0.679

GnomAD3 exomes

AF:

0.710

AC:

178267

AN:

250956

Hom.:

64742

AF XY:

0.701

AC XY:

94996

AN XY:

135606

show subpopulations

Gnomad AFR exome

AF:

0.556

Gnomad AMR exome

AF:

0.808

Gnomad ASJ exome

AF:

0.696

Gnomad EAS exome

AF:

0.581

Gnomad SAS exome

AF:

0.532

Gnomad FIN exome

AF:

0.799

Gnomad NFE exome

AF:

0.756

Gnomad OTH exome

AF:

0.717

GnomAD4 exome

AF:

0.735

AC:

1073912

AN:

1461126

Hom.:

398661

Cov.:

AF XY:

0.729

AC XY:

530178

AN XY:

726918

show subpopulations

Gnomad4 AFR exome

AF:

0.550

Gnomad4 AMR exome

AF:

0.800

Gnomad4 ASJ exome

AF:

0.692

Gnomad4 EAS exome

AF:

0.628

Gnomad4 SAS exome

AF:

0.541

Gnomad4 FIN exome

AF:

0.793

Gnomad4 NFE exome

AF:

0.757

Gnomad4 OTH exome

AF:

0.700

GnomAD4 genome

AF:

0.690

AC:

104914

AN:

152140

Hom.:

36959

Cov.:

AF XY:

0.689

AC XY:

51251

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.559

Gnomad4 AMR

AF:

0.737

Gnomad4 ASJ

AF:

0.693

Gnomad4 EAS

AF:

0.578

Gnomad4 SAS

AF:

0.545

Gnomad4 FIN

AF:

0.811

Gnomad4 NFE

AF:

0.757

Gnomad4 OTH

AF:

0.679

Alfa

AF:

0.735

Hom.:

13412

Bravo

AF:

0.682

TwinsUK

AF:

0.767

AC:

2845

ALSPAC

AF:

0.766

AC:

2951

ESP6500AA

AF:

0.566

AC:

2491

ESP6500EA

AF:

0.755

AC:

6486

ExAC

AF:

0.704

AC:

85411

Asia WGS

AF:

0.514

AC:

1787

AN:

3476

EpiCase

AF:

0.738

EpiControl

AF:

0.729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.14

BayesDel_noAF

Pathogenic

0.57

CADD

Pathogenic

DANN

Uncertain

0.98

Eigen

Benign

-0.014

Eigen_PC

Benign

-0.29

FATHMM_MKL

Benign

0.22

Vest4

0.12

GERP RS

2.4

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over