11-61018480-CAAGGGGAAAAGGAGAAAGG-CAAGGGGAAAAGGAGAAAGGAAGGGGAAAAGGAGAAAGG

Variant names:

• chr11-61018480-C-CAAGGGGAAAAGGAGAAAGG
• rs55799216
• NM_006725.5:c.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006725.5(CD6):​c.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 886,616 control chromosomes in the GnomAD database, including 11,498 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, 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.

• Frequency:
  • Genomes: 𝑓 0.22 (4264 hom., cov: 28)
  • Exomes 𝑓: 0.10 (7234 hom.)
• Consequence: CD6 NM_006725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 1 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]

ENSG00000303405 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

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.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG		intron	N/A	NP_006716.3	P30203-1
	CD6	NM_001254750.2		c.1741+473_1741+491dupGAAAAGGAGAAAGGAAGGG		intron	N/A	NP_001241679.1	P30203-4
	CD6	NM_001254751.2		c.1714+473_1714+491dupGAAAAGGAGAAAGGAAGGG		intron	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.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG		intron	N/A	ENSP00000323280.7	P30203-1
	CD6	ENST00000352009.9	TSL:1	c.1741+473_1741+491dupGAAAAGGAGAAAGGAAGGG		intron	N/A	ENSP00000340628.5	P30203-4
	CD6	ENST00000452451.6	TSL:1	c.1714+473_1714+491dupGAAAAGGAGAAAGGAAGGG		intron	N/A	ENSP00000390676.2	P30203-5

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32419 AN: 150796 Hom.: 4256 Cov.: 28

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.103 AC: 75844 AN: 735702 Hom.: 7234 Cov.: 11 AF XY: 0.105 AC XY: 39464 AN XY: 374196

African (AFR) AF: 0.309 AC: 5001 AN: 16198

American (AMR) AF: 0.0998 AC: 2551 AN: 25562

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 2347 AN: 17104

East Asian (EAS) AF: 0.0579 AC: 1868 AN: 32242

South Asian (SAS) AF: 0.107 AC: 5737 AN: 53866

European-Finnish (FIN) AF: 0.101 AC: 4508 AN: 44574

Middle Eastern (MID) AF: 0.192 AC: 764 AN: 3984

European-Non Finnish (NFE) AF: 0.0957 AC: 48537 AN: 507196

Other (OTH) AF: 0.130 AC: 4531 AN: 34976

GnomAD4 genome AF: 0.215 AC: 32461 AN: 150914 Hom.: 4264 Cov.: 28 AF XY: 0.209 AC XY: 15424 AN XY: 73680

African (AFR) AF: 0.375 AC: 15265 AN: 40760

American (AMR) AF: 0.144 AC: 2184 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3464

East Asian (EAS) AF: 0.0778 AC: 401 AN: 5154

South Asian (SAS) AF: 0.157 AC: 751 AN: 4770

European-Finnish (FIN) AF: 0.120 AC: 1260 AN: 10478

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11247 AN: 67814

Other (OTH) AF: 0.214 AC: 448 AN: 2094

Alfa AF: 0.149 Hom.: 42

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

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

dbSNP: rs55799216;

hg19: chr11-60785952;

COSMIC: COSV107372222;

COSMIC: COSV107372222;