Variant chr7-144232680-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001001802.3(OR2A42):c.164A>C(p.His55Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000073 ( 0 hom., cov: 15)

Exomes 𝑓: 0.00089 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

OR2A42
NM_001001802.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.36

Variant links:

Genes affected

OR2A42 (HGNC:31230): (olfactory receptor family 2 subfamily A member 42) 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]

OR2A42 links:

ARHGEF35-AS1 (HGNC:41292): (ARHGEF35 antisense RNA 1)

ARHGEF35-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2A42	NM_001001802.3 linkuse as main transcript	c.164A>C	p.His55Pro	missense_variant	3/3	ENST00000641810.1
ARHGEF35-AS1	NR_126022.1 linkuse as main transcript	n.493+24876T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2A42	ENST00000641810.1 linkuse as main transcript	c.164A>C	p.His55Pro	missense_variant	3/3		NM_001001802.3	P1
ARHGEF35-AS1	ENST00000460955.5 linkuse as main transcript	n.493+24876T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

110120

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000427

Gnomad MID

AF:

0.00360

Gnomad NFE

AF:

0.0000752

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000890

AC:

559

AN:

627972

Hom.:

Cov.:

AF XY:

0.000846

AC XY:

285

AN XY:

336690

show subpopulations

Gnomad4 AFR exome

AF:

0.000760

Gnomad4 AMR exome

AF:

0.000194

Gnomad4 ASJ exome

AF:

0.000645

Gnomad4 EAS exome

AF:

0.000767

Gnomad4 SAS exome

AF:

0.000202

Gnomad4 FIN exome

AF:

0.000388

Gnomad4 NFE exome

AF:

0.00120

Gnomad4 OTH exome

AF:

0.000767

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000726

AC:

AN:

110202

Hom.:

Cov.:

AF XY:

0.0000955

AC XY:

AN XY:

52354

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000427

Gnomad4 NFE

AF:

0.0000753

Gnomad4 OTH

AF:

0.00

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

Nov 19, 2022

The c.164A>C (p.H55P) alteration is located in exon 1 (coding exon 1) of the OR2A42 gene. This alteration results from a A to C substitution at nucleotide position 164, causing the histidine (H) at amino acid position 55 to be replaced by a proline (P). 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

BayesDel_addAF

Benign

-0.19

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.96

Eigen

Benign

-0.21

Eigen_PC

Benign

-0.17

FATHMM_MKL

Pathogenic

0.98

M_CAP

Benign

0.015

MetaRNN

Uncertain

0.71

D;D

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

D;D

PrimateAI

Benign

0.26

PROVEAN

Pathogenic

-7.6

.;D

REVEL

Benign

0.17

Sift

Uncertain

0.0030

.;D

Sift4G

Pathogenic

0.0010

.;D

Vest4

0.73

MutPred

0.72

Gain of glycosylation at H55 (P = 0.0717);Gain of glycosylation at H55 (P = 0.0717);

MVP

0.10

ClinPred

0.90

GERP RS

2.8

gMVP

0.38

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