rs11230563

Variant names:

• chr11-61008737-C-A
• rs11230563
• NM_006725.5:c.673C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-61008737-C-A
• chr11-61008737-C-G
• chr11-61008737-C-T

Variant summary

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

The NM_006725.5(CD6):​c.673C>A​(p.Arg225Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 34)
• Consequence: CD6 NM_006725.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.938
• Publications: 113 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 2 ACMG points.

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

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.673C>A	p.Arg225Arg	synonymous	Exon 4 of 13	NP_006716.3
	CD6	NM_001254750.2		c.673C>A	p.Arg225Arg	synonymous	Exon 4 of 11	NP_001241679.1
	CD6	NM_001254751.2		c.673C>A	p.Arg225Arg	synonymous	Exon 4 of 11	NP_001241680.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD6	ENST00000313421.11	TSL:1 MANE Select	c.673C>A	p.Arg225Arg	synonymous	Exon 4 of 13	ENSP00000323280.7
	CD6	ENST00000352009.9	TSL:1	c.673C>A	p.Arg225Arg	synonymous	Exon 4 of 11	ENSP00000340628.5
	CD6	ENST00000452451.6	TSL:1	c.673C>A	p.Arg225Arg	synonymous	Exon 4 of 11	ENSP00000390676.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 59

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 40485

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	20
DANN	Benign	0.69
PhyloP100		0.94
PromoterAI		-0.018	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.50		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.50		Position offset: 2

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

Other links and lift over

dbSNP: rs11230563; hg19: chr11-60776209;