11-60995102-C-T

Variant names:

• chr11-60995102-C-T
• rs2283263
• NM_006725.5:c.50-11472C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006725.5(CD6):​c.50-11472C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 151,808 control chromosomes in the GnomAD database, including 7,448 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 0.27 (7448 hom., cov: 31)
• Consequence: CD6 NM_006725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD6	NM_006725.5	MANE Select	c.50-11472C>T		intron	N/A	NP_006716.3
	CD6	NM_001254750.2		c.50-11472C>T		intron	N/A	NP_001241679.1
	CD6	NM_001254751.2		c.50-11472C>T		intron	N/A	NP_001241680.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD6	ENST00000313421.11	TSL:1 MANE Select	c.50-11472C>T		intron	N/A	ENSP00000323280.7
	CD6	ENST00000352009.9	TSL:1	c.50-11472C>T		intron	N/A	ENSP00000340628.5
	CD6	ENST00000452451.6	TSL:1	c.50-11472C>T		intron	N/A	ENSP00000390676.2

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41368 AN: 151694 Hom.: 7440 Cov.: 31

Gnomad AFR AF: 0.0650

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.273 AC: 41376 AN: 151808 Hom.: 7448 Cov.: 31 AF XY: 0.287 AC XY: 21271 AN XY: 74150

African (AFR) AF: 0.0648 AC: 2685 AN: 41426

American (AMR) AF: 0.417 AC: 6365 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3468

East Asian (EAS) AF: 0.559 AC: 2896 AN: 5178

South Asian (SAS) AF: 0.443 AC: 2126 AN: 4804

European-Finnish (FIN) AF: 0.477 AC: 4980 AN: 10440

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21065 AN: 67918

Other (OTH) AF: 0.244 AC: 514 AN: 2110

Alfa AF: 0.295 Hom.: 2976

Bravo AF: 0.256

Asia WGS AF: 0.469 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2283263; hg19: chr11-60762574;