3-122098766-G-A

Variant names:

• chr3-122098766-G-A
• rs2681416
• NM_175862.5:c.65-4746G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175862.5(CD86):​c.65-4746G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,116 control chromosomes in the GnomAD database, including 5,317 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 0.26 (5317 hom., cov: 32)
• Consequence: CD86 NM_175862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973
• Publications: 12 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD86	NM_175862.5	MANE Select	c.65-4746G>A		intron	N/A	NP_787058.5
	CD86	NM_006889.5		c.47-4746G>A		intron	N/A	NP_008820.4
	CD86	NM_176892.2		c.47-4746G>A		intron	N/A	NP_795711.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD86	ENST00000330540.7	TSL:1 MANE Select	c.65-4746G>A		intron	N/A	ENSP00000332049.2
	CD86	ENST00000393627.6	TSL:1	c.47-4746G>A		intron	N/A	ENSP00000377248.2
	CD86	ENST00000478741.1	TSL:5	c.50-4746G>A		intron	N/A	ENSP00000417195.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38816 AN: 151998 Hom.: 5314 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.250

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.255 AC: 38845 AN: 152116 Hom.: 5317 Cov.: 32 AF XY: 0.251 AC XY: 18646 AN XY: 74348

African (AFR) AF: 0.174 AC: 7239 AN: 41514

American (AMR) AF: 0.203 AC: 3099 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3470

East Asian (EAS) AF: 0.139 AC: 722 AN: 5180

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4820

European-Finnish (FIN) AF: 0.254 AC: 2689 AN: 10578

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21949 AN: 67952

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.292 Hom.: 4600

Bravo AF: 0.249

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.69
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2681416; hg19: chr3-121817613;