chr3-122084301-A-C

Variant names:

• chr3-122084301-A-C
• rs6805035
• NM_175862.5:c.15-7300A>C

Variant summary

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

The NM_175862.5(CD86):​c.15-7300A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,140 control chromosomes in the GnomAD database, including 1,176 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 0.12 (1176 hom., cov: 32)
• Consequence: CD86 NM_175862.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 2 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=-0.98).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD86	NM_175862.5	MANE Select	c.15-7300A>C		intron	N/A	NP_787058.5
	CD86	NM_006889.5		c.-5+6256A>C		intron	N/A	NP_008820.4
	CD86	NM_176892.2		c.-5+6256A>C		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.15-7300A>C		intron	N/A	ENSP00000332049.2
	CD86	ENST00000393627.6	TSL:1	c.-5+6256A>C		intron	N/A	ENSP00000377248.2
	CD86	ENST00000264468.9	TSL:5	c.-5+6256A>C		intron	N/A	ENSP00000264468.6

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18311 AN: 152022 Hom.: 1175 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0855

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.120 AC: 18316 AN: 152140 Hom.: 1176 Cov.: 32 AF XY: 0.118 AC XY: 8761 AN XY: 74370

African (AFR) AF: 0.127 AC: 5280 AN: 41518

American (AMR) AF: 0.0853 AC: 1304 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0639 AC: 222 AN: 3472

East Asian (EAS) AF: 0.00830 AC: 43 AN: 5182

South Asian (SAS) AF: 0.0504 AC: 243 AN: 4826

European-Finnish (FIN) AF: 0.149 AC: 1574 AN: 10566

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9279 AN: 67976

Other (OTH) AF: 0.104 AC: 220 AN: 2114

Alfa AF: 0.130 Hom.: 151

Bravo AF: 0.118

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.54
PhyloP100		-0.20
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: rs6805035; hg19: chr3-121803148;