Variant rs1050922 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_006725.5(CD6):c.1704A>G(p.Ser568Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 1,613,662 control chromosomes in the GnomAD database, including 317,416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.61 ( 29076 hom., cov: 30)

Exomes 𝑓: 0.62 ( 288340 hom. )

Consequence

CD6
NM_006725.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -5.40

Variant links:

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 links:

CD6 (HGNC:):

CD6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 11-61017880-A-G is Benign according to our data. Variant chr11-61017880-A-G is described in ClinVar as [Benign]. Clinvar id is 3059454.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-5.4 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD6	NM_006725.5 linkuse as main transcript	c.1704A>G	p.Ser568Ser	synonymous_variant	11/13	ENST00000313421.11	NP_006716.3	P30203-1Q8N4Q7Q6AZ88

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD6	ENST00000313421.11 linkuse as main transcript	c.1704A>G	p.Ser568Ser	synonymous_variant	11/13	1	NM_006725.5	ENSP00000323280.7		P30203-1

Frequencies

GnomAD3 genomes

AF:

0.607

AC:

92109

AN:

151728

Hom.:

29044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.652

Gnomad AMI

AF:

0.876

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.790

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.487

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.656

Gnomad OTH

AF:

0.657

GnomAD3 exomes

AF:

0.544

AC:

136776

AN:

251444

Hom.:

41258

AF XY:

0.549

AC XY:

74677

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.653

Gnomad AMR exome

AF:

0.364

Gnomad ASJ exome

AF:

0.806

Gnomad EAS exome

AF:

0.172

Gnomad SAS exome

AF:

0.400

Gnomad FIN exome

AF:

0.489

Gnomad NFE exome

AF:

0.665

Gnomad OTH exome

AF:

0.623

GnomAD4 exome

AF:

0.616

AC:

900834

AN:

1461816

Hom.:

288340

Cov.:

AF XY:

0.613

AC XY:

445818

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.655

Gnomad4 AMR exome

AF:

0.378

Gnomad4 ASJ exome

AF:

0.801

Gnomad4 EAS exome

AF:

0.154

Gnomad4 SAS exome

AF:

0.408

Gnomad4 FIN exome

AF:

0.497

Gnomad4 NFE exome

AF:

0.658

Gnomad4 OTH exome

AF:

0.615

GnomAD4 genome

AF:

0.607

AC:

92187

AN:

151846

Hom.:

29076

Cov.:

AF XY:

0.592

AC XY:

43905

AN XY:

74198

show subpopulations

Gnomad4 AFR

AF:

0.652

Gnomad4 AMR

AF:

0.504

Gnomad4 ASJ

AF:

0.790

Gnomad4 EAS

AF:

0.164

Gnomad4 SAS

AF:

0.381

Gnomad4 FIN

AF:

0.487

Gnomad4 NFE

AF:

0.656

Gnomad4 OTH

AF:

0.655

Alfa

AF:

0.660

Hom.:

67600

Bravo

AF:

0.615

Asia WGS

AF:

0.324

AC:

1128

AN:

3478

EpiCase

AF:

0.694

EpiControl

AF:

0.692

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CD6-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.039

DANN

Benign

0.30

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over