Variant 11-61018480-CAAGGGGAAAAGGAGAAAGG-CAAGGGGAAAAGGAGAAAGGAAGGGGAAAAGGAGAAAGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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. 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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CD6	NM_006725.5 link	c.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG		intron_variant		ENST00000313421.11	NP_006716.3	P30203-1Q8N4Q7Q6AZ88

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD6	ENST00000313421.11 link	c.1942+93_1942+111dupGAAAAGGAGAAAGGAAGGG		intron_variant		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

Gnomad4 AFR exome

AF:

0.309

Gnomad4 AMR exome

AF:

0.0998

Gnomad4 ASJ exome

AF:

0.137

Gnomad4 EAS exome

AF:

0.0579

Gnomad4 SAS exome

AF:

0.107

Gnomad4 FIN exome

AF:

0.101

Gnomad4 NFE exome

AF:

0.0957

Gnomad4 OTH exome

AF:

0.130

GnomAD4 genome

AF:

0.215

AC:

32461

AN:

150914

Hom.:

4264

Cov.:

AF XY:

0.209

AC XY:

15424

AN XY:

73680

show subpopulations

Gnomad4 AFR

AF:

0.375

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.179

Gnomad4 EAS

AF:

0.0778

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.120

Gnomad4 NFE

AF:

0.166

Gnomad4 OTH

AF:

0.214

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over