chr22-26623300-G-A
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_001886.3(CRYBA4):c.106G>A(p.Val36Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 1,614,012 control chromosomes in the GnomAD database, including 411 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 27 hom., cov: 32)
Exomes 𝑓: 0.021 ( 384 hom. )
Consequence
CRYBA4
NM_001886.3 missense
NM_001886.3 missense
Scores
6
12
Clinical Significance
Conservation
PhyloP100: 1.39
Genes affected
CRYBA4 (HGNC:2396): (crystallin beta A4) 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, is part of a gene cluster with beta-B1, beta-B2, and beta-B3. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
PM1
In a chain Beta-crystallin A4 (size 194) in uniprot entity CRBA4_HUMAN there are 10 pathogenic changes around while only 2 benign (83%) in NM_001886.3
BP4
Computational evidence support a benign effect (MetaRNN=0.0030172765).
BP6
Variant 22-26623300-G-A is Benign according to our data. Variant chr22-26623300-G-A is described in ClinVar as [Benign]. Clinvar id is 258485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-26623300-G-A is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0166 (2532/152278) while in subpopulation NFE AF= 0.025 (1703/68032). AF 95% confidence interval is 0.024. There are 27 homozygotes in gnomad4. There are 1220 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2532 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRYBA4 | NM_001886.3 | c.106G>A | p.Val36Met | missense_variant | 3/6 | ENST00000354760.4 | NP_001877.1 | |
CRYBA4 | XM_006724140.4 | c.121G>A | p.Val41Met | missense_variant | 5/8 | XP_006724203.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRYBA4 | ENST00000354760.4 | c.106G>A | p.Val36Met | missense_variant | 3/6 | 1 | NM_001886.3 | ENSP00000346805 | P1 | |
CRYBA4 | ENST00000466315.1 | n.55+665G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0166 AC: 2531AN: 152162Hom.: 27 Cov.: 32
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GnomAD3 exomes AF: 0.0174 AC: 4372AN: 251340Hom.: 60 AF XY: 0.0180 AC XY: 2441AN XY: 135848
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GnomAD4 exome AF: 0.0212 AC: 30922AN: 1461734Hom.: 384 Cov.: 32 AF XY: 0.0208 AC XY: 15138AN XY: 727190
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GnomAD4 genome AF: 0.0166 AC: 2532AN: 152278Hom.: 27 Cov.: 32 AF XY: 0.0164 AC XY: 1220AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 22, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Cataract 23 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at