11-60975316-A-G

Position:

• chr11-60975316-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006725.5(CD6):​c.49+3402A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,226 control chromosomes in the GnomAD database, including 48,012 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 0.79 (48012 hom., cov: 33)
• Consequence: CD6 NM_006725.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

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]

CD6 (HGNC:):

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 = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD6	NM_006725.5	c.49+3402A>G		intron_variant		ENST00000313421.11	NP_006716.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD6	ENST00000313421.11	c.49+3402A>G		intron_variant		1	NM_006725.5	ENSP00000323280.7

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120564 AN: 152108 Hom.: 47962 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.793 AC: 120671 AN: 152226 Hom.: 48012 Cov.: 33 AF XY: 0.798 AC XY: 59396 AN XY: 74422

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.786

Alfa AF: 0.773 Hom.: 6613

Bravo AF: 0.793

Asia WGS AF: 0.904 AC: 3144 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	2.6
DANN	Benign	0.64

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: rs2905504; hg19: chr11-60742788;