Genetic Variant CD6:c.1388-77C>T (chr11-61015636-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006725.5(CD6):c.1388-77C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 1,547,962 control chromosomes in the GnomAD database, including 236,968 homozygotes. 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: 𝑓 0.51 ( 21291 hom., cov: 31)

Exomes 𝑓: 0.55 ( 215677 hom. )

Consequence

CD6
NM_006725.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0190

Publications

14 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD6	NM_006725.5	MANE Select	c.1388-77C>T	intron	N/A	NP_006716.3
CD6	NM_001254750.2		c.1292-77C>T	intron	N/A	NP_001241679.1
CD6	NM_001254751.2		c.1387+1622C>T	intron	N/A	NP_001241680.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD6	ENST00000313421.11	TSL:1 MANE Select	c.1388-77C>T	intron	N/A	ENSP00000323280.7
CD6	ENST00000352009.9	TSL:1	c.1292-77C>T	intron	N/A	ENSP00000340628.5
CD6	ENST00000452451.6	TSL:1	c.1387+1622C>T	intron	N/A	ENSP00000390676.2

Frequencies

GnomAD3 genomes

AF:

0.513

AC:

78054

AN:

152008

Hom.:

21282

Cov.:

show subpopulations

Gnomad AFR

AF:

0.360

Gnomad AMI

AF:

0.469

Gnomad AMR

AF:

0.639

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.836

Gnomad SAS

AF:

0.679

Gnomad FIN

AF:

0.647

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.532

Gnomad OTH

AF:

0.490

GnomAD4 exome

AF:

0.548

AC:

764938

AN:

1395836

Hom.:

215677

Cov.:

AF XY:

0.549

AC XY:

380192

AN XY:

692050

show subpopulations

African (AFR)

AF:

0.350

AC:

11164

AN:

31906

American (AMR)

AF:

0.723

AC:

30398

AN:

42066

Ashkenazi Jewish (ASJ)

AF:

0.335

AC:

8125

AN:

24288

East Asian (EAS)

AF:

0.843

AC:

32877

AN:

38988

South Asian (SAS)

AF:

0.657

AC:

54498

AN:

82916

European-Finnish (FIN)

AF:

0.635

AC:

33138

AN:

52180

Middle Eastern (MID)

AF:

0.360

AC:

2012

AN:

5582

European-Non Finnish (NFE)

AF:

0.530

AC:

562008

AN:

1060118

Other (OTH)

AF:

0.532

AC:

30718

AN:

57792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

16631

33261

49892

66522

83153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16172

32344

48516

64688

80860

<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:

0.513

AC:

78092

AN:

152126

Hom.:

21291

Cov.:

AF XY:

0.525

AC XY:

39042

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.360

AC:

14920

AN:

41476

American (AMR)

AF:

0.640

AC:

9784

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

1182

AN:

3466

East Asian (EAS)

AF:

0.836

AC:

4321

AN:

5170

South Asian (SAS)

AF:

0.678

AC:

3270

AN:

4820

European-Finnish (FIN)

AF:

0.647

AC:

6859

AN:

10594

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.532

AC:

36199

AN:

67984

Other (OTH)

AF:

0.490

AC:

1034

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1852

3703

5555

7406

9258

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<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:

0.518

Hom.:

18592

Bravo

AF:

0.503

Asia WGS

AF:

0.705

AC:

2452

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.6

(source)

DANN

Benign

0.55

PhyloP100

-0.019

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over