22-26607993-G-C

Variant names:

• chr22-26607993-G-C
• rs147206089
• NM_001887.4:c.328C>G

Variant summary

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

The NM_001887.4(CRYBB1):​c.328C>G​(p.Arg110Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R110C) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CRYBB1 NM_001887.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08

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]

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]

ENSG00000286326 (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 rank	MANE	Protein	UniProt
CRYBB1	NM_001887.4	c.328C>G	p.Arg110Gly	missense_variant	Exon 4 of 6	ENST00000647684.1	NP_001878.1
CRYBB1	XM_011529899.4	c.328C>G	p.Arg110Gly	missense_variant	Exon 4 of 6		XP_011528201.1
CRYBA4	XM_006724140.4	c.-67G>C		5_prime_UTR_variant	Exon 3 of 8		XP_006724203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRYBB1	ENST00000647684.1	c.328C>G	p.Arg110Gly	missense_variant	Exon 4 of 6		NM_001887.4	ENSP00000497249.1
CRYBB1	ENST00000647569.1	n.140C>G		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000286326	ENST00000668614.1	n.228G>C		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Uncertain	0.058	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.38	T;T
Eigen	Benign	-0.047
Eigen_PC	Benign	-0.0096
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.81	.;T
M_CAP	Benign	0.081	D
MetaRNN	Uncertain	0.54	D;D
MetaSVM	Benign	-0.37	T
MutationAssessor	Uncertain	2.6	M;M
PrimateAI	Benign	0.37	T
PROVEAN	Uncertain	-3.0	.;D
REVEL	Uncertain	0.39
Sift	Benign	0.068	.;T
Sift4G	Benign	0.30	.;T
Polyphen		0.12	B;B
Vest4		0.69
MutPred		0.52		Loss of catalytic residue at R110 (P = 0.0216);Loss of catalytic residue at R110 (P = 0.0216);
MVP		0.86
MPC		0.43
ClinPred		0.82	D
GERP RS		2.5
Varity_R		0.38
gMVP		0.76

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

Other links and lift over

dbSNP: rs147206089; hg19: chr22-27003957;