Variant chr7-144232642-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001001802.3(OR2A42):c.202G>A(p.Val68Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000074 ( 1 hom., cov: 15)

Exomes 𝑓: 0.000092 ( 7 hom. )

Failed GnomAD Quality Control

Consequence

OR2A42
NM_001001802.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.56

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 Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.02929464).

BP6

Variant 7-144232642-C-T is Benign according to our data. Variant chr7-144232642-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2658124.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2A42	NM_001001802.3 link	c.202G>A	p.Val68Ile	missense_variant	3/3	ENST00000641810.1	NP_001001802.2	Q8NGT9
ARHGEF35-AS1	NR_126022.1 link	n.493+24838C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2A42	ENST00000641810.1 link	c.202G>A	p.Val68Ile	missense_variant	3/3		NM_001001802.3	ENSP00000493333.1		Q8NGT9

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

108576

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000163

Gnomad ASJ

AF:

0.00101

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000382

Gnomad OTH

AF:

0.000659

GnomAD3 exomes

AF:

0.000113

AC:

AN:

177746

Hom.:

AF XY:

0.000137

AC XY:

AN XY:

95102

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000167

Gnomad ASJ exome

AF:

0.00165

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000948

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000919

AC:

AN:

598182

Hom.:

Cov.:

AF XY:

0.0000929

AC XY:

AN XY:

322950

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000143

Gnomad4 ASJ exome

AF:

0.00146

Gnomad4 EAS exome

AF:

0.0000563

Gnomad4 SAS exome

AF:

0.0000467

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000264

Gnomad4 OTH exome

AF:

0.000190

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000737

AC:

AN:

108576

Hom.:

Cov.:

AF XY:

0.0000193

AC XY:

AN XY:

51918

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000163

Gnomad4 ASJ

AF:

0.00101

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000382

Gnomad4 OTH

AF:

0.000659

ExAC

AF:

0.0000795

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

ARHGEF35-AS1: BS2; OR2A42: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.0

DANN

Benign

0.66

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.013

M_CAP

Benign

0.0020

MetaRNN

Benign

0.029

T;T

MetaSVM

Benign

-0.93

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.33

.;N

REVEL

Benign

0.0070

Sift

Benign

0.41

.;T

Sift4G

Benign

0.43

.;T

Vest4

0.074

MutPred

0.40

Loss of glycosylation at S63 (P = 0.2896);Loss of glycosylation at S63 (P = 0.2896);

MVP

0.043

ClinPred

0.017

GERP RS

0.88

gMVP

0.054

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