11-61008714-CG-GA

Variant names:

• chr11-61008714-CG-GA
• NM_006725.5:c.650_651delCGinsGA
• CD6 p.Thr217Arg

Variant summary

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

The NM_006725.5(CD6):​c.650_651delCGinsGA​(p.Thr217Arg) 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T217M) has been classified as Benign.

• Frequency: Genomes: not found (cov: 34)
• Consequence: CD6 NM_006725.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.764
• Publications: 0 publications found

Genes affected

CD6 (HGNC:1691): (CD6 molecule) This gene encodes a protein found on the outer membrane of T-lymphocytes as well as some other immune cells. The encoded protein contains three scavenger receptor cysteine-rich (SRCR) domains and a binding site for an activated leukocyte cell adhesion molecule. The gene product is important for continuation of T cell activation. This gene may be associated with susceptibility to multiple sclerosis (PMID: 19525953, 21849685). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006725.5. 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
	CD6	NM_006725.5	MANE Select	c.650_651delCGinsGA	p.Thr217Arg	missense	N/A	NP_006716.3	P30203-1
	CD6	NM_001254750.2		c.650_651delCGinsGA	p.Thr217Arg	missense	N/A	NP_001241679.1	P30203-4
	CD6	NM_001254751.2		c.650_651delCGinsGA	p.Thr217Arg	missense	N/A	NP_001241680.1	P30203-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD6	ENST00000313421.11	TSL:1 MANE Select	c.650_651delCGinsGA	p.Thr217Arg	missense	N/A	ENSP00000323280.7	P30203-1
	CD6	ENST00000352009.9	TSL:1	c.650_651delCGinsGA	p.Thr217Arg	missense	N/A	ENSP00000340628.5	P30203-4
	CD6	ENST00000452451.6	TSL:1	c.650_651delCGinsGA	p.Thr217Arg	missense	N/A	ENSP00000390676.2	P30203-5

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.76

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: chr11-60776186;