2-208145688-CAAAAAAAAAAAAAA-CAA

Variant names:

• chr2-208145688-CAAAAAAAAAAAA-C
• rs554918356
• NM_005210.4:c.252+74_252+85delTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_005210.4(CRYGB):​c.252+74_252+85delTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000319 in 1,284,654 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000037 (0 hom., cov: 22)
  • Exomes 𝑓: 0.000032 (0 hom.)
• Consequence: CRYGB NM_005210.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 0 publications found

Genes affected

CRYGB (HGNC:2409): (crystallin gamma B) 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. Gamma-crystallins are a homogeneous group of highly symmetrical, monomeric proteins typically lacking connecting peptides and terminal extensions. They are differentially regulated after early development. Four gamma-crystallin genes (gamma-A through gamma-D) and three pseudogenes (gamma-E, gamma-F, gamma-G) are tandemly organized in a genomic segment as a gene cluster. Whether due to aging or mutations in specific genes, gamma-crystallins have been involved in cataract formation. [provided by RefSeq, Jul 2008]

CRYGB Gene-Disease associations (from GenCC):

• early-onset anterior polar cataract

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• early-onset lamellar cataract

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• total early-onset cataract

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• cataract 39 multiple types

  Inheritance: AD Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ENSG00000295187 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 39 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005210.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYGB	NM_005210.4	MANE Select	c.252+74_252+85delTTTTTTTTTTTT		intron	N/A	NP_005201.2	P07316
	LOC100507443	NR_038437.1		n.221+8521_221+8532delAAAAAAAAAAAA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYGB	ENST00000260988.5	TSL:1 MANE Select	c.252+74_252+85delTTTTTTTTTTTT		intron	N/A	ENSP00000260988.4	P07316
	ENSG00000295187	ENST00000728538.1		n.224+8510_224+8521delAAAAAAAAAAAA		intron	N/A
	ENSG00000295187	ENST00000728539.1		n.241+8510_241+8521delAAAAAAAAAAAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000374 AC: 2 AN: 53464 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.0000683

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000203

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000317 AC: 39 AN: 1231198 Hom.: 0 AF XY: 0.0000350 AC XY: 21 AN XY: 600846

African (AFR) AF: 0.00 AC: 0 AN: 26856

American (AMR) AF: 0.000273 AC: 7 AN: 25676

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17846

East Asian (EAS) AF: 0.00 AC: 0 AN: 33468

South Asian (SAS) AF: 0.0000491 AC: 3 AN: 61106

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30918

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3282

European-Non Finnish (NFE) AF: 0.0000265 AC: 26 AN: 981946

Other (OTH) AF: 0.0000599 AC: 3 AN: 50100

GnomAD4 genome AF: 0.0000374 AC: 2 AN: 53456 Hom.: 0 Cov.: 22 AF XY: 0.0000803 AC XY: 2 AN XY: 24914

African (AFR) AF: 0.0000682 AC: 1 AN: 14664

American (AMR) AF: 0.000203 AC: 1 AN: 4932

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1370

East Asian (EAS) AF: 0.00 AC: 0 AN: 1476

South Asian (SAS) AF: 0.00 AC: 0 AN: 1198

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1768

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 86

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 26880

Other (OTH) AF: 0.00 AC: 0 AN: 676

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs554918356; hg19: chr2-209010412;