11-61004618-C-T

Position:

• chr11-61004618-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.50-1956C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,158 control chromosomes in the GnomAD database, including 33,663 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 0.66 (33627 hom., cov: 31)
  • Exomes 𝑓: 0.66 (36 hom.)
• Consequence: CD6 NM_006725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

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]

LOC105369326 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD6	NM_006725.5	c.50-1956C>T		intron_variant		ENST00000313421.11
LOC105369326	XR_950155.3	n.393G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD6	ENST00000313421.11	c.50-1956C>T		intron_variant		1	NM_006725.5	P2

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100591 AN: 151874 Hom.: 33596 Cov.: 31

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.661 AC: 111 AN: 168 Hom.: 36 Cov.: 0 AF XY: 0.677 AC XY: 88 AN XY: 130

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.693

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.662 AC: 100671 AN: 151990 Hom.: 33627 Cov.: 31 AF XY: 0.666 AC XY: 49458 AN XY: 74288

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.640

Alfa AF: 0.644 Hom.: 64689

Bravo AF: 0.664

Asia WGS AF: 0.710 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2237997; hg19: chr11-60772090;