dbSNP rs9282641: CD86:c.-129G>A (chr3-122077921-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000393627.6(CD86):c.-129G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 985,330 control chromosomes in the GnomAD database, including 3,529 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 0.070 ( 439 hom., cov: 32)

Exomes 𝑓: 0.085 ( 3090 hom. )

Consequence

CD86
ENST00000393627.6 5_prime_UTR

Scores

Splicing: ADA: 0.00002264

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.755

Publications

69 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:

ENSG00000306536 (HGNC:):

ENSG00000306536 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD86	NM_175862.5 link	c.15-13680G>A		intron_variant	Intron 1 of 6	ENST00000330540.7	NP_787058.5	P42081-1A8K632

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD86	ENST00000330540.7 link	c.15-13680G>A		intron_variant	Intron 1 of 6	1	NM_175862.5	ENSP00000332049.2		P42081-1

Frequencies

GnomAD3 genomes

AF:

0.0702

AC:

10676

AN:

152112

Hom.:

438

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0387

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0686

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0959

Gnomad FIN

AF:

0.0868

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.0873

Gnomad OTH

AF:

0.0769

GnomAD4 exome

AF:

0.0846

AC:

70507

AN:

833100

Hom.:

3090

Cov.:

AF XY:

0.0849

AC XY:

32666

AN XY:

384734

show subpopulations

African (AFR)

AF:

0.0337

AC:

532

AN:

15786

American (AMR)

AF:

0.0650

AC:

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

632

AN:

5156

East Asian (EAS)

AF:

0.000551

AC:

AN:

3632

South Asian (SAS)

AF:

0.109

AC:

1790

AN:

16460

European-Finnish (FIN)

AF:

0.102

AC:

AN:

304

Middle Eastern (MID)

AF:

0.102

AC:

166

AN:

1620

European-Non Finnish (NFE)

AF:

0.0855

AC:

65104

AN:

761856

Other (OTH)

AF:

0.0801

AC:

2186

AN:

27302

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

3107

6214

9320

12427

15534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0701

AC:

10673

AN:

152230

Hom.:

439

Cov.:

AF XY:

0.0710

AC XY:

5286

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0385

AC:

1601

AN:

41536

American (AMR)

AF:

0.0686

AC:

1048

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

474

AN:

3470

East Asian (EAS)

AF:

0.000771

AC:

AN:

5188

South Asian (SAS)

AF:

0.0958

AC:

461

AN:

4814

European-Finnish (FIN)

AF:

0.0868

AC:

919

AN:

10588

Middle Eastern (MID)

AF:

0.137

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0873

AC:

5942

AN:

68026

Other (OTH)

AF:

0.0756

AC:

160

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

524

1047

1571

2094

2618

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0838

Hom.:

2574

Bravo

AF:

0.0665

Asia WGS

AF:

0.0480

AC:

167

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.1

(source)

DANN

Benign

0.63

PhyloP100

0.76

PromoterAI

-0.056

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000023

dbscSNV1_RF

Benign

0.0

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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rs9282641

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