chr11-60993058-C-T

Variant names:

• chr11-60993058-C-T
• rs11230553
• NM_006725.5:c.50-13516C>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.50-13516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,828 control chromosomes in the GnomAD database, including 4,430 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 0.24 (4430 hom., cov: 30)
• Consequence: CD6 NM_006725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD6	NM_006725.5	c.50-13516C>T		intron_variant	Intron 1 of 12	ENST00000313421.11	NP_006716.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD6	ENST00000313421.11	c.50-13516C>T		intron_variant	Intron 1 of 12	1	NM_006725.5	ENSP00000323280.7

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36240 AN: 151708 Hom.: 4426 Cov.: 30

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.239 AC: 36256 AN: 151828 Hom.: 4430 Cov.: 30 AF XY: 0.236 AC XY: 17502 AN XY: 74182

African (AFR) AF: 0.248 AC: 10257 AN: 41388

American (AMR) AF: 0.225 AC: 3426 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 539 AN: 3466

East Asian (EAS) AF: 0.312 AC: 1605 AN: 5152

South Asian (SAS) AF: 0.242 AC: 1158 AN: 4786

European-Finnish (FIN) AF: 0.193 AC: 2037 AN: 10546

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16279 AN: 67920

Other (OTH) AF: 0.243 AC: 512 AN: 2108

Alfa AF: 0.238 Hom.: 7326

Bravo AF: 0.243

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.42
PhyloP100		0.34
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: rs11230553; hg19: chr11-60760530;