chr22-25225624-C-T

Variant names:

• chr22-25225624-C-T
• rs5752084
• NM_000496.3:c.173+588C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000496.3(CRYBB2):​c.173+588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,066 control chromosomes in the GnomAD database, including 18,834 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (18834 hom., cov: 32)
• Consequence: CRYBB2 NM_000496.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

CRYBB2 (HGNC:2398): (crystallin beta B2) 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, is part of a gene cluster with beta-A4, beta-B1, and beta-B3. A chain-terminating mutation was found to cause type 2 cerulean cataracts. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRYBB2	NM_000496.3	c.173+588C>T		intron_variant	Intron 3 of 5	ENST00000398215.3	NP_000487.1
CRYBB2	XM_006724141.4	c.173+588C>T		intron_variant	Intron 3 of 5		XP_006724204.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRYBB2	ENST00000398215.3	c.173+588C>T		intron_variant	Intron 3 of 5	1	NM_000496.3	ENSP00000381273.2
CRYBB2	ENST00000651629.1	c.173+588C>T		intron_variant	Intron 3 of 5			ENSP00000498905.1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73731 AN: 151948 Hom.: 18818 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.485 AC: 73775 AN: 152066 Hom.: 18834 Cov.: 32 AF XY: 0.492 AC XY: 36577 AN XY: 74326

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.524

Alfa AF: 0.505 Hom.: 9478

Bravo AF: 0.486

Asia WGS AF: 0.728 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.41

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: rs5752084; hg19: chr22-25621591;