11-60995102-C-T

Position:

• chr11-60995102-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD6	NM_006725.5	c.50-11472C>T		intron_variant		ENST00000313421.11	NP_006716.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD6	ENST00000313421.11	c.50-11472C>T		intron_variant		1	NM_006725.5	ENSP00000323280	P2

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

Gnomad4 AFR AF: 0.0648

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.244

Alfa AF: 0.301 Hom.: 1948

Bravo AF: 0.256

Asia WGS AF: 0.469 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs2283263; hg19: chr11-60762574;