11-60975316-A-G

Variant names:

• chr11-60975316-A-G
• rs2905504
• NM_006725.5:c.49+3402A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.92).
• 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 rank	MANE	Protein	UniProt
CD6	NM_006725.5	c.49+3402A>G		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.49+3402A>G		intron_variant	Intron 1 of 12	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

African (AFR) AF: 0.796 AC: 33068 AN: 41538

American (AMR) AF: 0.827 AC: 12650 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2643 AN: 3468

East Asian (EAS) AF: 0.982 AC: 5095 AN: 5188

South Asian (SAS) AF: 0.830 AC: 4003 AN: 4824

European-Finnish (FIN) AF: 0.813 AC: 8609 AN: 10586

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52084 AN: 68010

Other (OTH) AF: 0.786 AC: 1659 AN: 2112

Alfa AF: 0.774 Hom.: 6861

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
PhyloP100		0.32
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: rs2905504; hg19: chr11-60742788;