GeneBe

rs78198409

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 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

Publications

0 publications found
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]
CNGB3 Gene-Disease associations (from GenCC):
  • achromatopsia 3
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
  • CNGB3-related retinopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • cone dystrophy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • achromatopsia
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • severe early-childhood-onset retinal dystrophy
    Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019098.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CNGB3
NM_019098.5
MANE Select
c.211+29_211+34delAAAAAA
intron
N/ANP_061971.3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CNGB3
ENST00000320005.6
TSL:1 MANE Select
c.211+29_211+34delAAAAAA
intron
N/AENSP00000316605.5Q9NQW8-1
CNGB3-AS1
ENST00000519041.1
TSL:3
n.449-21215_449-21210delTTTTTT
intron
N/A
CNGB3
ENST00000519777.1
TSL:2
n.193+29_193+34delAAAAAA
intron
N/A

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
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
29998
American (AMR)
AF:
0.0000265
AC:
1
AN:
37802
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24144
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37496
South Asian (SAS)
AF:
0.00
AC:
0
AN:
76466
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
42580
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5270
European-Non Finnish (NFE)
AF:
9.52e-7
AC:
1
AN:
1050228
Other (OTH)
AF:
0.00
AC:
0
AN:
56278
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.13

Splicing

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

Publications

Other links and lift over

dbSNP: rs78198409; hg19: chr8-87751848; API