chr8-86574893-CAT-C

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

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.405
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 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 UniProt
CNGB3NM_019098.5 linkuse as main transcriptc.*909_*910del 3_prime_UTR_variant 18/18 ENST00000320005.6
CNGB3XM_011517138.3 linkuse as main transcriptc.*909_*910del 3_prime_UTR_variant 16/16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CNGB3ENST00000320005.6 linkuse as main transcriptc.*909_*910del 3_prime_UTR_variant 18/181 NM_019098.5 P1Q9NQW8-1
CNGB3ENST00000517327.5 linkuse as main transcriptc.276+3794_276+3795del intron_variant 3
CNGB3ENST00000681546.1 linkuse as main transcriptn.3159_3160del non_coding_transcript_exon_variant 13/13
CNGB3ENST00000681746.1 linkuse as main transcriptc.*1750_*1751del 3_prime_UTR_variant, NMD_transcript_variant 19/19

Frequencies

GnomAD3 genomes
AF:
0.0842
AC:
12806
AN:
152040
Hom.:
579
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0791
Gnomad AMI
AF:
0.0855
Gnomad AMR
AF:
0.0611
Gnomad ASJ
AF:
0.0622
Gnomad EAS
AF:
0.0995
Gnomad SAS
AF:
0.0748
Gnomad FIN
AF:
0.108
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.0898
Gnomad OTH
AF:
0.0766
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
4
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.0843
AC:
12824
AN:
152158
Hom.:
578
Cov.:
31
AF XY:
0.0849
AC XY:
6316
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.0791
Gnomad4 AMR
AF:
0.0611
Gnomad4 ASJ
AF:
0.0622
Gnomad4 EAS
AF:
0.0998
Gnomad4 SAS
AF:
0.0759
Gnomad4 FIN
AF:
0.108
Gnomad4 NFE
AF:
0.0898
Gnomad4 OTH
AF:
0.0773
Alfa
AF:
0.0967
Hom.:
80
Bravo
AF:
0.0817
Asia WGS
AF:
0.120
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 submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Achromatopsia Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3217489; hg19: chr8-87587121; COSMIC: COSV60683935; API