8-86739620-GTTTTTT-GTTTT

Variant names:

• chr8-86739620-GTT-G
• rs78198409
• NM_019098.5:c.211+33_211+34delAA

Variant summary

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

The NM_019098.5(CNGB3):​c.211+33_211+34delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0418 in 1,471,490 control chromosomes in the GnomAD database, including 206 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.056 (194 hom., cov: 0)
  • Exomes 𝑓: 0.040 (12 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-GTT-G is Benign according to our data. Variant chr8-86739620-GTT-G is described in ClinVar as [Benign]. Clinvar id is 1267752.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNGB3	NM_019098.5	c.211+33_211+34delAA		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+33_211+34delAA		intron_variant	Intron 2 of 17	1	NM_019098.5	ENSP00000316605.5
ENSG00000254115	ENST00000519041.1	n.449-21215_449-21214delTT		intron_variant	Intron 1 of 2	3
CNGB3	ENST00000519777.1	n.193+33_193+34delAA		intron_variant	Intron 2 of 3	2
CNGB3	ENST00000681746.1	n.211+33_211+34delAA		intron_variant	Intron 2 of 18			ENSP00000505959.1

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 7144 AN: 128806 Hom.: 195 Cov.: 0

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0721

GnomAD4 exome AF: 0.0405 AC: 54318 AN: 1342674 Hom.: 12 AF XY: 0.0409 AC XY: 27330 AN XY: 667488

Gnomad4 AFR exome AF: 0.0694

Gnomad4 AMR exome AF: 0.0819

Gnomad4 ASJ exome AF: 0.0553

Gnomad4 EAS exome AF: 0.110

Gnomad4 SAS exome AF: 0.0427

Gnomad4 FIN exome AF: 0.0626

Gnomad4 NFE exome AF: 0.0337

Gnomad4 OTH exome AF: 0.0476

GnomAD4 genome AF: 0.0555 AC: 7150 AN: 128816 Hom.: 194 Cov.: 0 AF XY: 0.0581 AC XY: 3589 AN XY: 61800

Gnomad4 AFR AF: 0.0705

Gnomad4 AMR AF: 0.0736

Gnomad4 ASJ AF: 0.0697

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0476

Gnomad4 FIN AF: 0.0622

Gnomad4 NFE AF: 0.0360

Gnomad4 OTH AF: 0.0705

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 12, 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;