Variant chrX-151739696-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_005140.3(CNGA2):c.338G>T(p.Gly113Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00643 in 1,209,865 control chromosomes in the GnomAD database, including 22 homozygotes. There are 2,632 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0050 ( 3 hom., 157 hem., cov: 23)

Exomes 𝑓: 0.0066 ( 19 hom. 2475 hem. )

Consequence

CNGA2
NM_005140.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.245

Variant links:

Genes affected

CNGA2 (HGNC:2149): (cyclic nucleotide gated channel subunit alpha 2) The protein encoded by this gene represents the alpha subunit of a cyclic nucleotide-gated olfactory channel. The encoded protein contains a carboxy-terminal leucine zipper that mediates channel formation. [provided by RefSeq, Jan 2010]

CNGA2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0054856837).

BP6

Variant X-151739696-G-T is Benign according to our data. Variant chrX-151739696-G-T is described in ClinVar as [Benign]. Clinvar id is 728382.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-151739696-G-T is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNGA2	NM_005140.3 link	c.338G>T	p.Gly113Val	missense_variant	4/7	ENST00000329903.5	NP_005131.1	Q16280B3KXY3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CNGA2	ENST00000329903.5 link	c.338G>T	p.Gly113Val	missense_variant	4/7	5	NM_005140.3	ENSP00000328478.4		Q16280

Frequencies

GnomAD3 genomes

AF:

0.00502

AC:

561

AN:

111724

Hom.:

Cov.:

AF XY:

0.00463

AC XY:

157

AN XY:

33884

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00256

Gnomad ASJ

AF:

0.0155

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00454

Gnomad FIN

AF:

0.000823

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.00796

Gnomad OTH

AF:

0.0107

GnomAD3 exomes

AF:

0.00571

AC:

1047

AN:

183234

Hom.:

AF XY:

0.00672

AC XY:

455

AN XY:

67704

show subpopulations

Gnomad AFR exome

AF:

0.000684

Gnomad AMR exome

AF:

0.00321

Gnomad ASJ exome

AF:

0.0150

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00703

Gnomad FIN exome

AF:

0.00100

Gnomad NFE exome

AF:

0.00784

Gnomad OTH exome

AF:

0.0104

GnomAD4 exome

AF:

0.00658

AC:

7223

AN:

1098088

Hom.:

Cov.:

AF XY:

0.00681

AC XY:

2475

AN XY:

363450

show subpopulations

Gnomad4 AFR exome

AF:

0.000833

Gnomad4 AMR exome

AF:

0.00332

Gnomad4 ASJ exome

AF:

0.0158

Gnomad4 EAS exome

AF:

0.0000331

Gnomad4 SAS exome

AF:

0.00758

Gnomad4 FIN exome

AF:

0.00195

Gnomad4 NFE exome

AF:

0.00699

Gnomad4 OTH exome

AF:

0.00718

GnomAD4 genome

AF:

0.00502

AC:

561

AN:

111777

Hom.:

Cov.:

AF XY:

0.00462

AC XY:

157

AN XY:

33947

show subpopulations

Gnomad4 AFR

AF:

0.00104

Gnomad4 AMR

AF:

0.00256

Gnomad4 ASJ

AF:

0.0155

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00417

Gnomad4 FIN

AF:

0.000823

Gnomad4 NFE

AF:

0.00796

Gnomad4 OTH

AF:

0.0106

Alfa

AF:

0.00833

Hom.:

376

Bravo

AF:

0.00495

TwinsUK

AF:

0.00620

AC:

ALSPAC

AF:

0.00485

AC:

ESP6500AA

AF:

0.000522

AC:

ESP6500EA

AF:

0.00817

AC:

ExAC

AF:

0.00650

AC:

789

EpiCase

AF:

0.0110

EpiControl

AF:

0.0127

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Benign

0.96

DEOGEN2

Benign

0.10

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.69

M_CAP

Benign

0.047

MetaRNN

Benign

0.0055

MetaSVM

Uncertain

-0.17

MutationAssessor

Benign

1.5

PrimateAI

Benign

0.35

PROVEAN

Benign

-0.31

REVEL

Benign

0.19

Sift

Benign

0.41

Sift4G

Benign

0.32

Polyphen

0.013

Vest4

0.13

MVP

0.84

MPC

0.080

ClinPred

0.010

GERP RS

2.8

Varity_R

0.060

gMVP

0.57

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