11-119300340-T-TCA

Variant names:

• chr11-119300340-T-TCA
• rs3833768
• NM_005188.4:c.*559_*560insCA

Variant summary

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

The NM_005188.4(CBL):​c.*559_*560insCA variant causes a 3 prime UTR 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.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CBL NM_005188.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 3 publications found

Genes affected

CBL (HGNC:1541): (Cbl proto-oncogene) This gene is a proto-oncogene that encodes a RING finger E3 ubiquitin ligase. The encoded protein is one of the enzymes required for targeting substrates for degradation by the proteasome. This protein mediates the transfer of ubiquitin from ubiquitin conjugating enzymes (E2) to specific substrates. This protein also contains an N-terminal phosphotyrosine binding domain that allows it to interact with numerous tyrosine-phosphorylated substrates and target them for proteasome degradation. As such it functions as a negative regulator of many signal transduction pathways. This gene has been found to be mutated or translocated in many cancers including acute myeloid leukaemia, and expansion of CGG repeats in the 5' UTR has been associated with Jacobsen syndrome. Mutations in this gene are also the cause of Noonan syndrome-like disorder. [provided by RefSeq, Jul 2016]

CBL Gene-Disease associations (from GenCC):

• CBL-related disorder

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics
• juvenile myelomonocytic leukemia

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• Noonan syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005188.4. 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
	CBL	NM_005188.4	MANE Select	c.*559_*560insCA		3_prime_UTR	Exon 16 of 16	NP_005179.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CBL	ENST00000264033.6	TSL:1 MANE Select	c.*559_*560insCA		3_prime_UTR	Exon 16 of 16	ENSP00000264033.3	P22681
	CBL	ENST00000634840.1	TSL:5	c.*559_*560insCA		3_prime_UTR	Exon 15 of 15	ENSP00000489324.1	A0A0U1RR39
	CBL	ENST00000634586.1	TSL:5	c.2575+705_2575+706insCA		intron	N/A	ENSP00000489218.1	A0A0U1RQX8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 258804 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 131506

African (AFR) AF: 0.00 AC: 0 AN: 7288

American (AMR) AF: 0.00 AC: 0 AN: 10108

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9352

East Asian (EAS) AF: 0.00 AC: 0 AN: 23560

South Asian (SAS) AF: 0.00 AC: 0 AN: 4262

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21386

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1318

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 164702

Other (OTH) AF: 0.00 AC: 0 AN: 16828

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs3833768; hg19: chr11-119171050;