GeneBe

rs78198409

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_019098.5(CNGB3):​c.211+29_211+34delAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000147 in 1,360,262 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

CNGB3
NM_019098.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.129
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CNGB3NM_019098.5 linkc.211+29_211+34delAAAAAA intron_variant Intron 2 of 17 ENST00000320005.6 NP_061971.3 Q9NQW8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CNGB3ENST00000320005.6 linkc.211+29_211+34delAAAAAA intron_variant Intron 2 of 17 1 NM_019098.5 ENSP00000316605.5 Q9NQW8-1
ENSG00000254115ENST00000519041.1 linkn.449-21215_449-21210delTTTTTT intron_variant Intron 1 of 2 3
CNGB3ENST00000519777.1 linkn.193+29_193+34delAAAAAA intron_variant Intron 2 of 3 2
CNGB3ENST00000681746.1 linkn.211+29_211+34delAAAAAA intron_variant Intron 2 of 18 ENSP00000505959.1 A0A5J6DSN8

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000147
AC:
2
AN:
1360262
Hom.:
0
AF XY:
0.00000296
AC XY:
2
AN XY:
676428
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000265
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.52e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-87751848; API