8-86739620-GTTTTTT-GTTTTTTTT

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_019098.5(CNGB3):​c.211+33_211+34dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00041 (0 hom., cov: 0)
  • Exomes 𝑓: 0.016 (1 hom.)
• Consequence: CNGB3 NM_019098.5 intron
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0165 (21945/1330878) while in subpopulation SAS AF= 0.0446 (3271/73364). AF 95% confidence interval is 0.0433. There are 1 homozygotes in gnomad4_exome. There are 11740 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNGB3	NM_019098.5	c.211+33_211+34dupAA		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+35insAA		intron_variant	Intron 2 of 17	1	NM_019098.5	ENSP00000316605.5
ENSG00000254115	ENST00000519041.1	n.449-21216_449-21215insTT		intron_variant	Intron 1 of 2	3
CNGB3	ENST00000519777.1	n.193+34_193+35insAA		intron_variant	Intron 2 of 3	2
CNGB3	ENST00000681746.1	n.211+34_211+35insAA		intron_variant	Intron 2 of 18			ENSP00000505959.1

Frequencies

GnomAD3 genomes AF: 0.000411 AC: 53 AN: 128862 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000402

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000463

Gnomad ASJ AF: 0.000637

Gnomad EAS AF: 0.000224

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00124

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000349

Gnomad OTH AF: 0.000571

GnomAD4 exome AF: 0.0165 AC: 21945 AN: 1330878 Hom.: 1 Cov.: 0 AF XY: 0.0177 AC XY: 11740 AN XY: 661476

Gnomad4 AFR exome AF: 0.0337

Gnomad4 AMR exome AF: 0.0285

Gnomad4 ASJ exome AF: 0.0300

Gnomad4 EAS exome AF: 0.0181

Gnomad4 SAS exome AF: 0.0446

Gnomad4 FIN exome AF: 0.0199

Gnomad4 NFE exome AF: 0.0130

Gnomad4 OTH exome AF: 0.0177

GnomAD4 genome AF: 0.000411 AC: 53 AN: 128872 Hom.: 0 Cov.: 0 AF XY: 0.000356 AC XY: 22 AN XY: 61814

Gnomad4 AFR AF: 0.000402

Gnomad4 AMR AF: 0.000463

Gnomad4 ASJ AF: 0.000637

Gnomad4 EAS AF: 0.000225

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00124

Gnomad4 NFE AF: 0.000349

Gnomad4 OTH AF: 0.000568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;