11-61018480-CAAGGGGAAAAGGAGAAAGG-CAAGGGGAAAAGGAGAAAGGAAGGGGAAAAGGAGAAAGG
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
NM_006725.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.104
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]
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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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.215 AC: 32419AN: 150796Hom.: 4256 Cov.: 28
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GnomAD4 exome AF: 0.103 AC: 75844AN: 735702Hom.: 7234 Cov.: 11 AF XY: 0.105 AC XY: 39464AN XY: 374196
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GnomAD4 genome AF: 0.215 AC: 32461AN: 150914Hom.: 4264 Cov.: 28 AF XY: 0.209 AC XY: 15424AN XY: 73680
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at