Variant X-151739710-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_005140.3(CNGA2):c.352G>C(p.Asp118His) variant causes a missense change. The variant allele was found at a frequency of 0.00191 in 1,209,783 control chromosomes in the GnomAD database, including 37 homozygotes. There are 614 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.010 ( 19 hom., 321 hem., cov: 23)

Exomes 𝑓: 0.0011 ( 18 hom. 293 hem. )

Consequence

CNGA2
NM_005140.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.61

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004060149).

BP6

Variant X-151739710-G-C is Benign according to our data. Variant chrX-151739710-G-C is described in ClinVar as [Benign]. Clinvar id is 780737.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0101 (1132/111770) while in subpopulation AFR AF= 0.0354 (1089/30745). AF 95% confidence interval is 0.0337. There are 19 homozygotes in gnomad4. There are 321 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 19 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNGA2	NM_005140.3 linkuse as main transcript	c.352G>C	p.Asp118His	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 linkuse as main transcript	c.352G>C	p.Asp118His	missense_variant	4/7	5	NM_005140.3	ENSP00000328478.4		Q16280

Frequencies

GnomAD3 genomes

AF:

0.0100

AC:

1121

AN:

111716

Hom.:

Cov.:

AF XY:

0.00915

AC XY:

310

AN XY:

33876

show subpopulations

Gnomad AFR

AF:

0.0351

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00322

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:

0.0000564

Gnomad OTH

AF:

0.00399

GnomAD3 exomes

AF:

0.00286

AC:

523

AN:

182967

Hom.:

AF XY:

0.00168

AC XY:

113

AN XY:

67457

show subpopulations

Gnomad AFR exome

AF:

0.0363

Gnomad AMR exome

AF:

0.00120

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000105

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000368

Gnomad OTH exome

AF:

0.00177

GnomAD4 exome

AF:

0.00107

AC:

1175

AN:

1098013

Hom.:

Cov.:

AF XY:

0.000806

AC XY:

293

AN XY:

363373

show subpopulations

Gnomad4 AFR exome

AF:

0.0383

Gnomad4 AMR exome

AF:

0.00128

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000129

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000202

Gnomad4 OTH exome

AF:

0.00197

GnomAD4 genome

AF:

0.0101

AC:

1132

AN:

111770

Hom.:

Cov.:

AF XY:

0.00946

AC XY:

321

AN XY:

33940

show subpopulations

Gnomad4 AFR

AF:

0.0354

Gnomad4 AMR

AF:

0.00322

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000564

Gnomad4 OTH

AF:

0.00394

Alfa

AF:

0.00183

Hom.:

Bravo

AF:

0.0115

ESP6500AA

AF:

0.0402

AC:

154

ESP6500EA

AF:

0.000149

AC:

ExAC

AF:

0.00326

AC:

396

EpiCase

AF:

0.000164

EpiControl

AF:

0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

0.092

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.12

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.14

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.68

MetaRNN

Benign

0.0041

MetaSVM

Uncertain

0.41

MutationAssessor

Uncertain

2.2

PrimateAI

Benign

0.38

PROVEAN

Benign

-1.0

REVEL

Uncertain

0.48

Sift

Benign

0.074

Sift4G

Benign

0.062

Polyphen

0.93

Vest4

0.17

MVP

0.83

MPC

0.30

ClinPred

0.012

GERP RS

4.5

Varity_R

0.22

gMVP

0.30

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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