Genetic Variant CD86:c.*1260G>C (chr3-122120794-G-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.*1260G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,660 control chromosomes in the GnomAD database, including 1,420 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 0.14 ( 1416 hom., cov: 32)

Exomes 𝑓: 0.12 ( 4 hom. )

Consequence

CD86
NM_175862.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.400

Publications

50 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:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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	Effect	Exon Rank	Protein	UniProt
CD86	NM_175862.5	MANE Select	c.*1260G>C	3_prime_UTR	Exon 7 of 7	NP_787058.5
CD86	NM_006889.5		c.*1260G>C	3_prime_UTR	Exon 7 of 7	NP_008820.4	P42081-3
CD86	NM_176892.2		c.*1260G>C	3_prime_UTR	Exon 6 of 6	NP_795711.2	P42081-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD86	ENST00000330540.7	TSL:1 MANE Select	c.*1260G>C		3_prime_UTR	Exon 7 of 7	ENSP00000332049.2	P42081-1
	CD86	ENST00000264468.9	TSL:5	c.*1260G>C		3_prime_UTR	Exon 6 of 6	ENSP00000264468.6	P42081-4

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20599

AN:

152088

Hom.:

1415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.0511

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.141

GnomAD4 exome

AF:

0.123

AC:

AN:

454

Hom.:

Cov.:

AF XY:

0.121

AC XY:

AN XY:

248

show subpopulations

African (AFR)

AF:

0.0714

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

AN:

East Asian (EAS)

AF:

0.0152

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.107

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.161

AC:

AN:

274

Other (OTH)

AF:

0.0556

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.135

AC:

20609

AN:

152206

Hom.:

1416

Cov.:

AF XY:

0.135

AC XY:

10048

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.128

AC:

5328

AN:

41514

American (AMR)

AF:

0.106

AC:

1616

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

561

AN:

3472

East Asian (EAS)

AF:

0.0508

AC:

263

AN:

5178

South Asian (SAS)

AF:

0.111

AC:

536

AN:

4822

European-Finnish (FIN)

AF:

0.149

AC:

1578

AN:

10590

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10240

AN:

68014

Other (OTH)

AF:

0.139

AC:

294

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

924

1848

2771

3695

4619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.0670

Hom.:

Bravo

AF:

0.131

Asia WGS

AF:

0.0920

AC:

319

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.48

(source)

DANN

Benign

0.47

PhyloP100

-0.40

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over