17-29249281-T-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005208.5(CRYBA1):c.96+75T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,047,860 control chromosomes in the GnomAD database, including 8,810 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.13 ( 1456 hom., cov: 31)
Exomes 𝑓: 0.12 ( 7354 hom. )
Consequence
CRYBA1
NM_005208.5 intron
NM_005208.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.158
Publications
7 publications found
Genes affected
CRYBA1 (HGNC:2394): (crystallin beta A1) Crystallins are separated into two classes: taxon-specific, or enzyme, and ubiquitous. The latter class constitutes the major proteins of vertebrate eye lens and maintains the transparency and refractive index of the lens. Since lens central fiber cells lose their nuclei during development, these crystallins are made and then retained throughout life, making them extremely stable proteins. Mammalian lens crystallins are divided into alpha, beta, and gamma families; beta and gamma crystallins are also considered as a superfamily. Alpha and beta families are further divided into acidic and basic groups. Seven protein regions exist in crystallins: four homologous motifs, a connecting peptide, and N- and C-terminal extensions. Beta-crystallins, the most heterogeneous, differ by the presence of the C-terminal extension (present in the basic group, none in the acidic group). Beta-crystallins form aggregates of different sizes and are able to self-associate to form dimers or to form heterodimers with other beta-crystallins. This gene, a beta acidic group member, encodes two proteins (crystallin, beta A3 and crystallin, beta A1) from a single mRNA, the latter protein is 17 aa shorter than crystallin, beta A3 and is generated by use of an alternate translation initiation site. Deletion of exons 3 and 4 causes the autosomal dominant disease 'zonular cataract with sutural opacities'. [provided by RefSeq, Jul 2008]
CRYBA1 Gene-Disease associations (from GenCC):
- cataract 10 multiple typesInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- early-onset lamellar cataractInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- early-onset nuclear cataractInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- early-onset posterior polar cataractInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- early-onset sutural cataractInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 17-29249281-T-G is Benign according to our data. Variant chr17-29249281-T-G is described in ClinVar as [Benign]. Clinvar id is 1232029.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19755AN: 151866Hom.: 1454 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
19755
AN:
151866
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 AF: 0.116 AC: 103678AN: 895876Hom.: 7354 AF XY: 0.117 AC XY: 54576AN XY: 468090 show subpopulations
GnomAD4 exome
AF:
AC:
103678
AN:
895876
Hom.:
AF XY:
AC XY:
54576
AN XY:
468090
show subpopulations
African (AFR)
AF:
AC:
3754
AN:
22490
American (AMR)
AF:
AC:
5304
AN:
42040
Ashkenazi Jewish (ASJ)
AF:
AC:
2104
AN:
21962
East Asian (EAS)
AF:
AC:
11774
AN:
37088
South Asian (SAS)
AF:
AC:
12529
AN:
74860
European-Finnish (FIN)
AF:
AC:
5628
AN:
50664
Middle Eastern (MID)
AF:
AC:
403
AN:
4646
European-Non Finnish (NFE)
AF:
AC:
57410
AN:
600522
Other (OTH)
AF:
AC:
4772
AN:
41604
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
4441
8881
13322
17762
22203
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.130 AC: 19779AN: 151984Hom.: 1456 Cov.: 31 AF XY: 0.132 AC XY: 9787AN XY: 74300 show subpopulations
GnomAD4 genome
AF:
AC:
19779
AN:
151984
Hom.:
Cov.:
31
AF XY:
AC XY:
9787
AN XY:
74300
show subpopulations
African (AFR)
AF:
AC:
7132
AN:
41462
American (AMR)
AF:
AC:
1619
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
366
AN:
3470
East Asian (EAS)
AF:
AC:
1534
AN:
5148
South Asian (SAS)
AF:
AC:
830
AN:
4814
European-Finnish (FIN)
AF:
AC:
1232
AN:
10550
Middle Eastern (MID)
AF:
AC:
13
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6639
AN:
67952
Other (OTH)
AF:
AC:
239
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
856
1711
2567
3422
4278
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
793
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Aug 03, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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