8-86574893-CAT-C
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_019098.5(CNGB3):c.*909_*910del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,158 control chromosomes in the GnomAD database, including 578 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.084 ( 578 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CNGB3
NM_019098.5 3_prime_UTR
NM_019098.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.405
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 8-86574893-CAT-C is Benign according to our data. Variant chr8-86574893-CAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 363853.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0927 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNGB3 | NM_019098.5 | c.*909_*910del | 3_prime_UTR_variant | 18/18 | ENST00000320005.6 | NP_061971.3 | ||
CNGB3 | XM_011517138.3 | c.*909_*910del | 3_prime_UTR_variant | 16/16 | XP_011515440.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNGB3 | ENST00000320005.6 | c.*909_*910del | 3_prime_UTR_variant | 18/18 | 1 | NM_019098.5 | ENSP00000316605 | P1 | ||
CNGB3 | ENST00000517327.5 | c.276+3794_276+3795del | intron_variant | 3 | ENSP00000428329 | |||||
CNGB3 | ENST00000681546.1 | n.3159_3160del | non_coding_transcript_exon_variant | 13/13 | ||||||
CNGB3 | ENST00000681746.1 | c.*1750_*1751del | 3_prime_UTR_variant, NMD_transcript_variant | 19/19 | ENSP00000505959 |
Frequencies
GnomAD3 genomes AF: 0.0842 AC: 12806AN: 152040Hom.: 579 Cov.: 31
GnomAD3 genomes
AF:
AC:
12806
AN:
152040
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 4Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
4
Hom.:
AF XY:
AC XY:
0
AN XY:
2
Gnomad4 NFE exome
AF:
GnomAD4 genome AF: 0.0843 AC: 12824AN: 152158Hom.: 578 Cov.: 31 AF XY: 0.0849 AC XY: 6316AN XY: 74378
GnomAD4 genome
AF:
AC:
12824
AN:
152158
Hom.:
Cov.:
31
AF XY:
AC XY:
6316
AN XY:
74378
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
416
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Stargardt Disease, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Achromatopsia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at