11-111911973-G-T

Variant names:

• chr11-111911973-G-T
• rs14133
• ENST00000526180.6:c.-224-25C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001885.3(CRYAB):​c.-198-51C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000838 in 357,878 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000084 (0 hom.)
• Consequence: CRYAB NM_001885.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.67
• Publications: 0 publications found

Genes affected

CRYAB (HGNC:2389): (crystallin alpha B) Mammalian lens crystallins are divided into alpha, beta, and gamma families. Alpha crystallins are composed of two gene products: alpha-A and alpha-B, for acidic and basic, respectively. Alpha crystallins can be induced by heat shock and are members of the small heat shock protein (HSP20) family. They act as molecular chaperones although they do not renature proteins and release them in the fashion of a true chaperone; instead they hold them in large soluble aggregates. These heterogeneous aggregates consist of 30-40 subunits; the alpha-A and alpha-B subunits have a 3:1 ratio, respectively. Two additional functions of alpha crystallins are an autokinase activity and participation in the intracellular architecture. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. Alpha-A and alpha-B gene products are differentially expressed; alpha-A is preferentially restricted to the lens and alpha-B is expressed widely in many tissues and organs. Elevated expression of alpha-B crystallin occurs in many neurological diseases; a missense mutation cosegregated in a family with a desmin-related myopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2019]

HSPB2 (HGNC:5247): (heat shock protein family B (small) member 2) The protein encoded by this gene belongs to the superfamily of small heat-shock proteins containing a conservative alpha-crystallin domain at the C-terminal part of the molecule. The protein is expressed preferentially in the heart and skeletal muscle. This protein regulates Myotonic Dystrophy Protein Kinase, which plays an important role in maintenance of muscle structure and function. [provided by RefSeq, Dec 2012]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001885.3. 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
	CRYAB	NM_001289807.1		c.-198-51C>A		intron	N/A	NP_001276736.1	P02511
	CRYAB	NM_001368245.1		c.-198-51C>A		intron	N/A	NP_001355174.1	P02511
	CRYAB	NM_001885.3		c.-198-51C>A		intron	N/A	NP_001876.1	P02511

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYAB	ENST00000526180.6	TSL:1	c.-224-25C>A		intron	N/A	ENSP00000436051.1	P02511
	CRYAB	ENST00000227251.7	TSL:5	c.-148C>A		5_prime_UTR	Exon 1 of 4	ENSP00000227251.3	P02511
	CRYAB	ENST00000651164.1		c.-159C>A		5_prime_UTR	Exon 1 of 4	ENSP00000498735.1	P02511

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000838 AC: 3 AN: 357878 Hom.: 0 Cov.: 0 AF XY: 0.00000532 AC XY: 1 AN XY: 187982

African (AFR) AF: 0.00 AC: 0 AN: 10638

American (AMR) AF: 0.00 AC: 0 AN: 15732

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11368

East Asian (EAS) AF: 0.00 AC: 0 AN: 23900

South Asian (SAS) AF: 0.00 AC: 0 AN: 39046

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20768

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1574

European-Non Finnish (NFE) AF: 0.0000140 AC: 3 AN: 214036

Other (OTH) AF: 0.00 AC: 0 AN: 20816

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	20
DANN	Benign	0.93
PhyloP100		2.7
PromoterAI		-0.16	Neutral

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

Other links and lift over

dbSNP: rs14133; hg19: chr11-111782697;