16-30353573-CC-TT

Variant names:

• chr16-30353573-CC-TT
• NM_006110.3:c.602_603delGGinsAA
• CD2BP2 p.Arg201Gln

Variant summary

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

The NM_006110.3(CD2BP2):​c.602_603delGGinsAA​(p.Arg201Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R201L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CD2BP2 NM_006110.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603
• Publications: 0 publications found

Genes affected

CD2BP2 (HGNC:1656): (CD2 cytoplasmic tail binding protein 2) This gene encodes a bi-functional protein. In the cytoplasm, the encoded protein binds the cytoplasmic tail of human surface antigen CD2 via its C-terminal GYF domain, and regulate CD2-triggered T lymphocyte activation. In the nucleus, this protein is a component of the U5 small nuclear ribonucleoprotein complex and is involved in RNA splicing. A pseudogene has been identified on chromosome 7. Alternative splicing results in multiple transcript variants but their biological validity has not been determined. [provided by RefSeq, Nov 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006110.3. 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
	CD2BP2	NM_006110.3	MANE Select	c.602_603delGGinsAA	p.Arg201Gln	missense	N/A	NP_006101.1	O95400
	CD2BP2	NM_001243646.2		c.602_603delGGinsAA	p.Arg201Gln	missense	N/A	NP_001230575.1	A0A024QZC1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD2BP2	ENST00000305596.8	TSL:1 MANE Select	c.602_603delGGinsAA	p.Arg201Gln	missense	N/A	ENSP00000304903.3	O95400
	CD2BP2	ENST00000569466.1	TSL:1	c.602_603delGGinsAA	p.Arg201Gln	missense	N/A	ENSP00000456935.1	O95400
	CD2BP2	ENST00000921036.1		c.602_603delGGinsAA	p.Arg201Gln	missense	N/A	ENSP00000591095.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.60

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-30364894;