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

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]

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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
CD6NM_006725.5 linkc.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
CD6ENST00000313421.11 linkc.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.:
28
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.:
11
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.:
28
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.:
42
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.

Other links and lift over

dbSNP: rs55799216; hg19: chr11-60785952; API