Variant 8-86578666-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_019098.5(CNGB3):c.2103+23C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00968 in 1,611,896 control chromosomes in the GnomAD database, including 678 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.039 ( 337 hom., cov: 32)

Exomes 𝑓: 0.0066 ( 341 hom. )

Consequence

CNGB3
NM_019098.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.316

Variant links:

Genes affected

CNGB3 (HGNC:2153): (cyclic nucleotide gated channel subunit beta 3) This gene encodes the beta subunit of a cyclic nucleotide-gated ion channel. The encoded beta subunit appears to play a role in modulation of channel function in cone photoreceptors. This heterotetrameric channel is necessary for sensory transduction, and mutations in this gene have been associated with achromatopsia 3, progressive cone dystrophy, and juvenile macular degeneration, also known as Stargardt Disease. [provided by RefSeq, Feb 2010]

CNGB3 links:

CNGB3 (HGNC:):

CNGB3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 8-86578666-G-C is Benign according to our data. Variant chr8-86578666-G-C is described in ClinVar as [Benign]. Clinvar id is 261085.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CNGB3	NM_019098.5 linkuse as main transcript	c.2103+23C>G		intron_variant		ENST00000320005.6	NP_061971.3	Q9NQW8-1
CNGB3	XM_011517138.3 linkuse as main transcript	c.1689+23C>G		intron_variant			XP_011515440.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CNGB3	ENST00000320005.6 linkuse as main transcript	c.2103+23C>G	intron_variant	1	NM_019098.5	ENSP00000316605.5	Q9NQW8-1
CNGB3	ENST00000517327.5 linkuse as main transcript	c.276+23C>G	intron_variant	3		ENSP00000428329.1	H0YAZ4
CNGB3	ENST00000681546.1 linkuse as main transcript	n.1923+23C>G	intron_variant
CNGB3	ENST00000681746.1 linkuse as main transcript	n.*514+23C>G	intron_variant			ENSP00000505959.1	A0A5J6DSN8

Frequencies

GnomAD3 genomes

AF:

0.0393

AC:

5977

AN:

152084

Hom.:

333

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0200

Gnomad ASJ

AF:

0.0271

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0133

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.0159

Gnomad NFE

AF:

0.00238

Gnomad OTH

AF:

0.0402

GnomAD3 exomes

AF:

0.0134

AC:

3351

AN:

250902

Hom.:

141

AF XY:

0.0113

AC XY:

1530

AN XY:

135648

show subpopulations

Gnomad AFR exome

AF:

0.128

Gnomad AMR exome

AF:

0.0101

Gnomad ASJ exome

AF:

0.0246

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0114

Gnomad FIN exome

AF:

0.000740

Gnomad NFE exome

AF:

0.00217

Gnomad OTH exome

AF:

0.00996

GnomAD4 exome

AF:

0.00658

AC:

9612

AN:

1459694

Hom.:

341

Cov.:

AF XY:

0.00644

AC XY:

4677

AN XY:

726254

show subpopulations

Gnomad4 AFR exome

AF:

0.129

Gnomad4 AMR exome

AF:

0.0110

Gnomad4 ASJ exome

AF:

0.0250

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0131

Gnomad4 FIN exome

AF:

0.000750

Gnomad4 NFE exome

AF:

0.00185

Gnomad4 OTH exome

AF:

0.0140

GnomAD4 genome

AF:

0.0394

AC:

5997

AN:

152202

Hom.:

337

Cov.:

AF XY:

0.0385

AC XY:

2867

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.127

Gnomad4 AMR

AF:

0.0200

Gnomad4 ASJ

AF:

0.0271

Gnomad4 EAS

AF:

0.00136

Gnomad4 SAS

AF:

0.0133

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00238

Gnomad4 OTH

AF:

0.0417

Alfa

AF:

0.00524

Hom.:

Bravo

AF:

0.0444

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

DANN

Benign

0.55

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