22-26601647-A-ATGTGGATAAACCATTCACCGTGTCGTACTAAGCTTGAGTTCTAACTAACATCAAGTAAGGATTGACTTCGAGAATTACTAGTGGTTACGAATTGTGACGGACAAGGACAGGGAGACACCAACAGAGACCCGGGAATCACTGAGGTATATTTTGTCCCTATCAGGTTCAGGGACAACCCGTCTCACCAACGGGATACAGTCGGACACACAGACTCCATCCCACCTCCCGTACGGGTCACCTGTATTCTAGGTGCGTCGAGCAAACGAGAATCAGAGGGGGGGAAACAGTTCGGACGTTTTCCAAGGTCAGTAGGACATAAGACTCGGTAAGGCTCT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001887.4(CRYBB1):c.575+231_575+232insAGAGCCTTACCGAGTCTTATGTCCTACTGACCTTGGAAAACGTCCGAACTGTTTCCCCCCCTCTGATTCTCGTTTGCTCGACGCACCTAGAATACAGGTGACCCGTACGGGAGGTGGGATGGAGTCTGTGTGTCCGACTGTATCCCGTTGGTGAGACGGGTTGTCCCTGAACCTGATAGGGACAAAATATACCTCAGTGATTCCCGGGTCTCTGTTGGTGTCTCCCTGTCCTTGTCCGTCACAATTCGTAACCACTAGTAATTCTCGAAGTCAATCCTTACTTGATGTTAGTTAGAACTCAAGCTTAGTACGACACGGTGAATGGTTTATCCACA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 30)
• Consequence: CRYBB1 NM_001887.4 intron
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -0.0830

Genes affected

CRYBB1 (HGNC:2397): (crystallin beta B1) 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 basic group member, undergoes extensive cleavage at its N-terminal extension during lens maturation. It is also a member of a gene cluster with beta-A4, beta-B2, and beta-B3. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRYBB1	NM_001887.4	c.575+231_575+232insAGAGCCTTACCGAGTCTTATGTCCTACTGACCTTGGAAAACGTCCGAACTGTTTCCCCCCCTCTGATTCTCGTTTGCTCGACGCACCTAGAATACAGGTGACCCGTACGGGAGGTGGGATGGAGTCTGTGTGTCCGACTGTATCCCGTTGGTGAGACGGGTTGTCCCTGAACCTGATAGGGACAAAATATACCTCAGTGATTCCCGGGTCTCTGTTGGTGTCTCCCTGTCCTTGTCCGTCACAATTCGTAACCACTAGTAATTCTCGAAGTCAATCCTTACTTGATGTTAGTTAGAACTCAAGCTTAGTACGACACGGTGAATGGTTTATCCACA		intron_variant		ENST00000647684.1
CRYBA4	XM_006724140.4	c.-239+4564_-239+4565insTGTGGATAAACCATTCACCGTGTCGTACTAAGCTTGAGTTCTAACTAACATCAAGTAAGGATTGACTTCGAGAATTACTAGTGGTTACGAATTGTGACGGACAAGGACAGGGAGACACCAACAGAGACCCGGGAATCACTGAGGTATATTTTGTCCCTATCAGGTTCAGGGACAACCCGTCTCACCAACGGGATACAGTCGGACACACAGACTCCATCCCACCTCCCGTACGGGTCACCTGTATTCTAGGTGCGTCGAGCAAACGAGAATCAGAGGGGGGGAAACAGTTCGGACGTTTTCCAAGGTCAGTAGGACATAAGACTCGGTAAGGCTCT		intron_variant
CRYBB1	XM_011529899.4	c.575+231_575+232insAGAGCCTTACCGAGTCTTATGTCCTACTGACCTTGGAAAACGTCCGAACTGTTTCCCCCCCTCTGATTCTCGTTTGCTCGACGCACCTAGAATACAGGTGACCCGTACGGGAGGTGGGATGGAGTCTGTGTGTCCGACTGTATCCCGTTGGTGAGACGGGTTGTCCCTGAACCTGATAGGGACAAAATATACCTCAGTGATTCCCGGGTCTCTGTTGGTGTCTCCCTGTCCTTGTCCGTCACAATTCGTAACCACTAGTAATTCTCGAAGTCAATCCTTACTTGATGTTAGTTAGAACTCAAGCTTAGTACGACACGGTGAATGGTTTATCCACA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRYBB1	ENST00000647684.1	c.575+231_575+232insAGAGCCTTACCGAGTCTTATGTCCTACTGACCTTGGAAAACGTCCGAACTGTTTCCCCCCCTCTGATTCTCGTTTGCTCGACGCACCTAGAATACAGGTGACCCGTACGGGAGGTGGGATGGAGTCTGTGTGTCCGACTGTATCCCGTTGGTGAGACGGGTTGTCCCTGAACCTGATAGGGACAAAATATACCTCAGTGATTCCCGGGTCTCTGTTGGTGTCTCCCTGTCCTTGTCCGTCACAATTCGTAACCACTAGTAATTCTCGAAGTCAATCCTTACTTGATGTTAGTTAGAACTCAAGCTTAGTACGACACGGTGAATGGTTTATCCACA		intron_variant			NM_001887.4	P1
	ENST00000668614.1	n.56+4564_56+4565insTGTGGATAAACCATTCACCGTGTCGTACTAAGCTTGAGTTCTAACTAACATCAAGTAAGGATTGACTTCGAGAATTACTAGTGGTTACGAATTGTGACGGACAAGGACAGGGAGACACCAACAGAGACCCGGGAATCACTGAGGTATATTTTGTCCCTATCAGGTTCAGGGACAACCCGTCTCACCAACGGGATACAGTCGGACACACAGACTCCATCCCACCTCCCGTACGGGTCACCTGTATTCTAGGTGCGTCGAGCAAACGAGAATCAGAGGGGGGGAAACAGTTCGGACGTTTTCCAAGGTCAGTAGGACATAAGACTCGGTAAGGCTCT		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 30

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 30

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Schizophrenia Uncertain:1

Uncertain significance, no assertion criteria provided

case-control

Department of Psychiatry, The University of Hong Kong

Nov 11, 2022

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-26997611;