8-86739620-GTTTTTT-GTTTTTTT

Variant names:

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

Variant summary

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

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

• Frequency:
  • Genomes: 𝑓 0.038 (265 hom., cov: 0)
  • Exomes 𝑓: 0.14 (15 hom.)
• 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-G-GT is Benign according to our data. Variant chr8-86739620-G-GT is described in ClinVar as [Benign]. Clinvar id is 1183444.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNGB3	NM_019098.5	c.211+34dupA		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+34_211+35insA		intron_variant	Intron 2 of 17	1	NM_019098.5	ENSP00000316605.5
ENSG00000254115	ENST00000519041.1	n.449-21216_449-21215insT		intron_variant	Intron 1 of 2	3
CNGB3	ENST00000519777.1	n.193+34_193+35insA		intron_variant	Intron 2 of 3	2
CNGB3	ENST00000681746.1	n.211+34_211+35insA		intron_variant	Intron 2 of 18			ENSP00000505959.1

Frequencies

GnomAD3 genomes AF: 0.0381 AC: 4902 AN: 128824 Hom.: 265 Cov.: 0

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0176

Gnomad ASJ AF: 0.00763

Gnomad EAS AF: 0.00134

Gnomad SAS AF: 0.00299

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.0224

Gnomad NFE AF: 0.00562

Gnomad OTH AF: 0.0320

GnomAD4 exome AF: 0.135 AC: 176248 AN: 1304352 Hom.: 15 Cov.: 0 AF XY: 0.136 AC XY: 88179 AN XY: 647800

Gnomad4 AFR exome AF: 0.156

Gnomad4 AMR exome AF: 0.112

Gnomad4 ASJ exome AF: 0.146

Gnomad4 EAS exome AF: 0.117

Gnomad4 SAS exome AF: 0.151

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.135

Gnomad4 OTH exome AF: 0.133

GnomAD4 genome AF: 0.0380 AC: 4898 AN: 128834 Hom.: 265 Cov.: 0 AF XY: 0.0381 AC XY: 2353 AN XY: 61792

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0176

Gnomad4 ASJ AF: 0.00763

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.00276

Gnomad4 FIN AF: 0.0104

Gnomad4 NFE AF: 0.00562

Gnomad4 OTH AF: 0.0318

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 07, 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;