11-61008631-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_006725.5(CD6):c.567T>C(p.Thr189=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,607,596 control chromosomes in the GnomAD database, including 15,687 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 2147 hom., cov: 33)
Exomes 𝑓: 0.13 ( 13540 hom. )
Consequence
CD6
NM_006725.5 synonymous
NM_006725.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.593
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 11-61008631-T-C is Benign according to our data. Variant chr11-61008631-T-C is described in ClinVar as [Benign]. Clinvar id is 3059657.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.593 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD6 | NM_006725.5 | c.567T>C | p.Thr189= | synonymous_variant | 4/13 | ENST00000313421.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD6 | ENST00000313421.11 | c.567T>C | p.Thr189= | synonymous_variant | 4/13 | 1 | NM_006725.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.157 AC: 23873AN: 152136Hom.: 2143 Cov.: 33
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GnomAD3 exomes AF: 0.131 AC: 30607AN: 234100Hom.: 2176 AF XY: 0.134 AC XY: 16974AN XY: 127130
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GnomAD4 exome AF: 0.133 AC: 193910AN: 1455342Hom.: 13540 Cov.: 31 AF XY: 0.135 AC XY: 97487AN XY: 723400
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GnomAD4 genome ? AF: 0.157 AC: 23904AN: 152254Hom.: 2147 Cov.: 33 AF XY: 0.153 AC XY: 11384AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CD6-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 01, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at