chr3-122069201-C-T

Variant names:

• chr3-122069201-C-T
• rs2715268
• NM_175862.5:c.14+13698C>T

Variant summary

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

The NM_175862.5(CD86):​c.14+13698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,950 control chromosomes in the GnomAD database, including 940 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 0.11 (940 hom., cov: 31)
• Consequence: CD86 NM_175862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD86	NM_175862.5	MANE Select	c.14+13698C>T		intron	N/A	NP_787058.5
	CD86	NM_001206925.2		c.-183+13698C>T		intron	N/A	NP_001193854.2
	CD86	NM_001206924.2		c.14+13698C>T		intron	N/A	NP_001193853.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD86	ENST00000330540.7	TSL:1 MANE Select	c.14+13698C>T		intron	N/A	ENSP00000332049.2
	CD86	ENST00000469710.5	TSL:2	c.-183+13698C>T		intron	N/A	ENSP00000418988.1
	CD86	ENST00000493101.5	TSL:2	c.14+13698C>T		intron	N/A	ENSP00000420230.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16156 AN: 151832 Hom.: 940 Cov.: 31

Gnomad AFR AF: 0.0806

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.106 AC: 16158 AN: 151950 Hom.: 940 Cov.: 31 AF XY: 0.104 AC XY: 7723 AN XY: 74262

African (AFR) AF: 0.0806 AC: 3340 AN: 41456

American (AMR) AF: 0.0774 AC: 1182 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3466

East Asian (EAS) AF: 0.00753 AC: 39 AN: 5178

South Asian (SAS) AF: 0.0483 AC: 232 AN: 4804

European-Finnish (FIN) AF: 0.148 AC: 1564 AN: 10550

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9237 AN: 67914

Other (OTH) AF: 0.0917 AC: 194 AN: 2116

Alfa AF: 0.121 Hom.: 137

Bravo AF: 0.102

Asia WGS AF: 0.0330 AC: 117 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	5.4
DANN	Benign	0.52
PhyloP100		0.052
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: rs2715268; hg19: chr3-121788048;