Genetic Variant NM_006725.5:c.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG (chr11-61018480-C-CAAGGGGAAAAGGAGAAAGG) – ACMG Classification: Benign (-8 pts)

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104

Publications

1 publications found

Variant links:

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]

CD6 links:

ENSG00000303405 (HGNC:):

ENSG00000303405 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD6	NM_006725.5 link	c.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG		intron_variant	Intron 12 of 12	ENST00000313421.11	NP_006716.3	P30203-1Q8N4Q7Q6AZ88

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD6	ENST00000313421.11 link	c.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG		intron_variant	Intron 12 of 12	1	NM_006725.5	ENSP00000323280.7		P30203-1

Frequencies

GnomAD3 genomes

AF:

0.215

AC:

32419

AN:

150796

Hom.:

4256

Cov.:

show subpopulations

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.:

AF XY:

0.105

AC XY:

39464

AN XY:

374196

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

3032

6064

9096

12128

15160

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

746

1492

2238

2984

3730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.215

AC:

32461

AN:

150914

Hom.:

4264

Cov.:

AF XY:

0.209

AC XY:

15424

AN XY:

73680

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11247

AN:

67814

Other (OTH)

AF:

0.214

AC:

448

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1110

2220

3330

4440

5550

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.149

Hom.:

Asia WGS

AF:

0.149

AC:

518

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.10

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over