chr8-86739620-GT-G

Variant names:

• chr8-86739620-GT-G
• rs78198409
• NM_019098.5:c.211+34delA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_019098.5(CNGB3):​c.211+34delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.36 (7096 hom., cov: 0)
  • Exomes 𝑓: 0.31 (316 hom.)
  • Failed GnomAD Quality Control
• Consequence: CNGB3 NM_019098.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.129

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]

ENSG00000254115 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-86739620-GT-G is Benign according to our data. Variant chr8-86739620-GT-G is described in ClinVar as [Benign]. Clinvar id is 1233884.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-86739620-GT-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNGB3	NM_019098.5	c.211+34delA		intron_variant	Intron 2 of 17	ENST00000320005.6	NP_061971.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNGB3	ENST00000320005.6	c.211+34delA		intron_variant	Intron 2 of 17	1	NM_019098.5	ENSP00000316605.5
ENSG00000254115	ENST00000519041.1	n.449-21215delT		intron_variant	Intron 1 of 2	3
CNGB3	ENST00000519777.1	n.193+34delA		intron_variant	Intron 2 of 3	2
CNGB3	ENST00000681746.1	n.211+34delA		intron_variant	Intron 2 of 18			ENSP00000505959.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 46359 AN: 128534 Hom.: 7108 Cov.: 0

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.284

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.344

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.306 AC: 407716 AN: 1332888 Hom.: 316 Cov.: 0 AF XY: 0.304 AC XY: 201331 AN XY: 662412

Gnomad4 AFR exome AF: 0.252

Gnomad4 AMR exome AF: 0.276

Gnomad4 ASJ exome AF: 0.280

Gnomad4 EAS exome AF: 0.278

Gnomad4 SAS exome AF: 0.267

Gnomad4 FIN exome AF: 0.295

Gnomad4 NFE exome AF: 0.314

Gnomad4 OTH exome AF: 0.301

GnomAD4 genome AF: 0.360 AC: 46339 AN: 128544 Hom.: 7096 Cov.: 0 AF XY: 0.359 AC XY: 22149 AN XY: 61660

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.342

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 19, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs78198409; hg19: chr8-87751848;