11-61015636-C-T

Position:

• chr11-61015636-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.1388-77C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 1,547,962 control chromosomes in the GnomAD database, including 236,968 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 0.51 (21291 hom., cov: 31)
  • Exomes 𝑓: 0.55 (215677 hom.)
• Consequence: CD6 NM_006725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD6	NM_006725.5	c.1388-77C>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.1388-77C>T		intron_variant		1	NM_006725.5	ENSP00000323280	P2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 78054 AN: 152008 Hom.: 21282 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.490

GnomAD4 exome AF: 0.548 AC: 764938 AN: 1395836 Hom.: 215677 Cov.: 22 AF XY: 0.549 AC XY: 380192 AN XY: 692050

Gnomad4 AFR exome AF: 0.350

Gnomad4 AMR exome AF: 0.723

Gnomad4 ASJ exome AF: 0.335

Gnomad4 EAS exome AF: 0.843

Gnomad4 SAS exome AF: 0.657

Gnomad4 FIN exome AF: 0.635

Gnomad4 NFE exome AF: 0.530

Gnomad4 OTH exome AF: 0.532

GnomAD4 genome AF: 0.513 AC: 78092 AN: 152126 Hom.: 21291 Cov.: 31 AF XY: 0.525 AC XY: 39042 AN XY: 74352

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.490

Alfa AF: 0.519 Hom.: 15295

Bravo AF: 0.503

Asia WGS AF: 0.705 AC: 2452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.55

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: rs2074229; hg19: chr11-60783108;