Genetic Variant CD86:c.*410T>C (chr3-122119944-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_175862.5(CD86):c.*410T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.60 ( 7830 hom., cov: 24)

Exomes 𝑓: 0.29 ( 1096 hom. )

Failed GnomAD Quality Control

Consequence

CD86
NM_175862.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.270

Publications

18 publications found

Variant links:

Genes affected

CD86 (HGNC:1705): (CD86 molecule) This gene encodes a type I membrane protein that is a member of the immunoglobulin superfamily. This protein is expressed by antigen-presenting cells, and it is the ligand for two proteins at the cell surface of T cells, CD28 antigen and cytotoxic T-lymphocyte-associated protein 4. Binding of this protein with CD28 antigen is a costimulatory signal for activation of the T-cell. Binding of this protein with cytotoxic T-lymphocyte-associated protein 4 negatively regulates T-cell activation and diminishes the immune response. Alternative splicing results in several transcript variants encoding different isoforms.[provided by RefSeq, May 2011]

CD86 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD86	NM_175862.5 link	c.*410T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000330540.7	NP_787058.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD86	ENST00000330540.7 link	c.*410T>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_175862.5	ENSP00000332049.2

Frequencies

GnomAD3 genomes

AF:

0.599

AC:

46305

AN:

77326

Hom.:

7824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.551

Gnomad AMI

AF:

0.608

Gnomad AMR

AF:

0.568

Gnomad ASJ

AF:

0.588

Gnomad EAS

AF:

0.721

Gnomad SAS

AF:

0.697

Gnomad FIN

AF:

0.609

Gnomad MID

AF:

0.583

Gnomad NFE

AF:

0.597

Gnomad OTH

AF:

0.594

GnomAD4 exome

AF:

0.294

AC:

5878

AN:

19980

Hom.:

1096

Cov.:

AF XY:

0.312

AC XY:

3125

AN XY:

10032

show subpopulations

African (AFR)

AF:

0.125

AC:

AN:

168

American (AMR)

AF:

0.152

AC:

188

AN:

1234

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

AN:

328

East Asian (EAS)

AF:

0.567

AC:

195

AN:

344

South Asian (SAS)

AF:

0.500

AC:

639

AN:

1278

European-Finnish (FIN)

AF:

0.319

AC:

255

AN:

800

Middle Eastern (MID)

AF:

0.283

AC:

AN:

European-Non Finnish (NFE)

AF:

0.285

AC:

4150

AN:

14556

Other (OTH)

AF:

0.285

AC:

346

AN:

1212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

180

360

541

721

901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.599

AC:

46319

AN:

77342

Hom.:

7830

Cov.:

AF XY:

0.602

AC XY:

23208

AN XY:

38530

show subpopulations

African (AFR)

AF:

0.551

AC:

7987

AN:

14498

American (AMR)

AF:

0.568

AC:

3706

AN:

6526

Ashkenazi Jewish (ASJ)

AF:

0.588

AC:

1067

AN:

1814

East Asian (EAS)

AF:

0.720

AC:

3125

AN:

4338

South Asian (SAS)

AF:

0.698

AC:

2661

AN:

3814

European-Finnish (FIN)

AF:

0.609

AC:

4016

AN:

6596

Middle Eastern (MID)

AF:

0.576

AC:

AN:

172

European-Non Finnish (NFE)

AF:

0.597

AC:

22661

AN:

37928

Other (OTH)

AF:

0.599

AC:

658

AN:

1098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1585

3170

4755

6340

7925

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.313

Hom.:

7881

Bravo

AF:

0.282

Asia WGS

AF:

0.641

AC:

1989

AN:

3110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

(source)

DANN

Benign

0.52

PhyloP100

-0.27

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over