rs1129055

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_175862.5(CD86):c.928G>A(p.Ala310Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,604,162 control chromosomes in the GnomAD database, including 71,297 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5761 hom., cov: 33)

Exomes 𝑓: 0.29 ( 65536 hom. )

Consequence

CD86
NM_175862.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.778

Publications

88 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.8654267E-5).

BP6

Variant 3-122119472-G-A is Benign according to our data. Variant chr3-122119472-G-A is described in ClinVar as Benign. ClinVar VariationId is 1227026.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175862.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CD86	NM_175862.5	MANE Select	c.928G>A	p.Ala310Thr	missense	Exon 7 of 7	NP_787058.5
CD86	NM_006889.5		c.910G>A	p.Ala304Thr	missense	Exon 7 of 7	NP_008820.4	P42081-3
CD86	NM_176892.2		c.766G>A	p.Ala256Thr	missense	Exon 6 of 6	NP_795711.2	P42081-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CD86	ENST00000330540.7	TSL:1 MANE Select	c.928G>A	p.Ala310Thr	missense	Exon 7 of 7	ENSP00000332049.2	P42081-1
CD86	ENST00000393627.6	TSL:1	c.910G>A	p.Ala304Thr	missense	Exon 7 of 7	ENSP00000377248.2	P42081-3
CD86	ENST00000478741.1	TSL:5	c.769G>A	p.Ala257Thr	missense	Exon 5 of 5	ENSP00000417195.1	H7C4F8

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39513

AN:

152020

Hom.:

5757

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.277

Gnomad EAS

AF:

0.597

Gnomad SAS

AF:

0.446

Gnomad FIN

AF:

0.322

Gnomad MID

AF:

0.298

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.251

GnomAD2 exomes

AF:

0.301

AC:

75387

AN:

250762

AF XY:

0.312

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.167

Gnomad ASJ exome

AF:

0.262

Gnomad EAS exome

AF:

0.602

Gnomad FIN exome

AF:

0.326

Gnomad NFE exome

AF:

0.270

Gnomad OTH exome

AF:

0.292

GnomAD4 exome

AF:

0.288

AC:

418110

AN:

1452022

Hom.:

65536

Cov.:

AF XY:

0.294

AC XY:

212357

AN XY:

722722

show subpopulations

African (AFR)

AF:

0.164

AC:

5442

AN:

33276

American (AMR)

AF:

0.173

AC:

7722

AN:

44608

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

6840

AN:

26056

East Asian (EAS)

AF:

0.639

AC:

25314

AN:

39600

South Asian (SAS)

AF:

0.443

AC:

38044

AN:

85868

European-Finnish (FIN)

AF:

0.320

AC:

17106

AN:

53400

Middle Eastern (MID)

AF:

0.277

AC:

1596

AN:

5752

European-Non Finnish (NFE)

AF:

0.270

AC:

298295

AN:

1103398

Other (OTH)

AF:

0.296

AC:

17751

AN:

60064

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.444

Heterozygous variant carriers

13569

27138

40706

54275

67844

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10080

20160

30240

40320

50400

<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

AF:

0.260

AC:

39519

AN:

152140

Hom.:

5761

Cov.:

AF XY:

0.267

AC XY:

19828

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.176

AC:

7308

AN:

41498

American (AMR)

AF:

0.206

AC:

3148

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.277

AC:

962

AN:

3470

East Asian (EAS)

AF:

0.596

AC:

3088

AN:

5178

South Asian (SAS)

AF:

0.446

AC:

2149

AN:

4822

European-Finnish (FIN)

AF:

0.322

AC:

3404

AN:

10564

Middle Eastern (MID)

AF:

0.288

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.274

AC:

18614

AN:

68008

Other (OTH)

AF:

0.258

AC:

544

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1468

2936

4403

5871

7339

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<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:

0.274

Hom.:

29451

Bravo

AF:

0.242

TwinsUK

AF:

0.266

AC:

985

ALSPAC

AF:

0.279

AC:

1076

ESP6500AA

AF:

0.172

AC:

756

ESP6500EA

AF:

0.260

AC:

2235

ExAC

AF:

0.305

AC:

37008

Asia WGS

AF:

0.509

AC:

1767

AN:

3478

EpiCase

AF:

0.270

EpiControl

AF:

0.269

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.7

(source)

DANN

Benign

0.93

DEOGEN2

Benign

0.35

Eigen

Benign

-0.33

Eigen_PC

Benign

-0.41

FATHMM_MKL

Benign

0.20

LIST_S2

Benign

0.64

MetaRNN

Benign

0.000039

MetaSVM

Benign

-0.92

MutationAssessor

Benign

1.4

PhyloP100

0.78

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.66

REVEL

Benign

0.031

Sift

Benign

0.18

Sift4G

Uncertain

0.037

Polyphen

0.0060

Vest4

0.077

MPC

0.31

ClinPred

0.018

GERP RS

3.2

Varity_R

0.044

gMVP

0.068

Mutation Taster

=81/19

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over