8-86739620-GTTTTTT-GTTTTTTTTT

Variant names:

• chr8-86739620-G-GTTT
• rs78198409
• NM_019098.5:c.211+32_211+34dupAAA

Variant summary

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

The NM_019098.5(CNGB3):​c.211+32_211+34dupAAA 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 0.000031 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0019 (0 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 = 0.00185 (2507/1354566) while in subpopulation SAS AF= 0.00628 (475/75664). AF 95% confidence interval is 0.00581. There are 0 homozygotes in gnomad4_exome. There are 1349 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+32_211+34dupAAA		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+35insAAA		intron_variant	Intron 2 of 17	1	NM_019098.5	ENSP00000316605.5
ENSG00000254115	ENST00000519041.1	n.449-21216_449-21215insTTT		intron_variant	Intron 1 of 2	3
CNGB3	ENST00000519777.1	n.193+34_193+35insAAA		intron_variant	Intron 2 of 3	2
CNGB3	ENST00000681746.1	n.211+34_211+35insAAA		intron_variant	Intron 2 of 18			ENSP00000505959.1

Frequencies

GnomAD3 genomes AF: 0.0000310 AC: 4 AN: 128882 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000287

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000772

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000332

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00185 AC: 2507 AN: 1354566 Hom.: 0 Cov.: 0 AF XY: 0.00200 AC XY: 1349 AN XY: 673372

Gnomad4 AFR exome AF: 0.00439

Gnomad4 AMR exome AF: 0.00413

Gnomad4 ASJ exome AF: 0.00376

Gnomad4 EAS exome AF: 0.00204

Gnomad4 SAS exome AF: 0.00628

Gnomad4 FIN exome AF: 0.00266

Gnomad4 NFE exome AF: 0.00127

Gnomad4 OTH exome AF: 0.00225

GnomAD4 genome AF: 0.0000310 AC: 4 AN: 128892 Hom.: 0 Cov.: 0 AF XY: 0.0000162 AC XY: 1 AN XY: 61824

Gnomad4 AFR AF: 0.0000287

Gnomad4 AMR AF: 0.0000771

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000332

Gnomad4 OTH AF: 0.00

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;