chr3-122074340-C-A

Variant names:

• chr3-122074340-C-A
• rs4308217
• NM_175862.5:c.15-17261C>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.15-17261C>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 152,138 control chromosomes in the GnomAD database, including 6,352 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 (6352 hom., cov: 31)
• Consequence: CD86 NM_175862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 28 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]

ENSG00000306536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 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.15-17261C>A		intron	N/A	NP_787058.5
	CD86	NM_001206925.2		c.-183+18837C>A		intron	N/A	NP_001193854.2
	CD86	NM_001206924.2		c.15-17261C>A		intron	N/A	NP_001193853.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD86	ENST00000330540.7	TSL:1 MANE Select	c.15-17261C>A		intron	N/A	ENSP00000332049.2
	CD86	ENST00000469710.5	TSL:2	c.-183+18837C>A		intron	N/A	ENSP00000418988.1
	CD86	ENST00000493101.5	TSL:2	c.15-17261C>A		intron	N/A	ENSP00000420230.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38839 AN: 152020 Hom.: 6343 Cov.: 31

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.255 AC: 38847 AN: 152138 Hom.: 6352 Cov.: 31 AF XY: 0.256 AC XY: 19006 AN XY: 74378

African (AFR) AF: 0.0736 AC: 3056 AN: 41536

American (AMR) AF: 0.449 AC: 6864 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3470

East Asian (EAS) AF: 0.136 AC: 703 AN: 5182

South Asian (SAS) AF: 0.162 AC: 781 AN: 4810

European-Finnish (FIN) AF: 0.300 AC: 3176 AN: 10582

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22490 AN: 67972

Other (OTH) AF: 0.283 AC: 597 AN: 2108

Alfa AF: 0.299 Hom.: 15179

Bravo AF: 0.262

Asia WGS AF: 0.149 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.43
PhyloP100		-0.30
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: rs4308217; hg19: chr3-121793187;