3-122119944-T-A

Variant names:

• chr3-122119944-T-A
• rs1915087
• NM_175862.5:c.*410T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_175862.5(CD86):​c.*410T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 24)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CD86 NM_175862.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 18 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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.*410T>A		3_prime_UTR	Exon 7 of 7	NP_787058.5
	CD86	NM_006889.5		c.*410T>A		3_prime_UTR	Exon 7 of 7	NP_008820.4
	CD86	NM_176892.2		c.*410T>A		3_prime_UTR	Exon 6 of 6	NP_795711.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD86	ENST00000330540.7	TSL:1 MANE Select	c.*410T>A		3_prime_UTR	Exon 7 of 7	ENSP00000332049.2
	CD86	ENST00000264468.9	TSL:5	c.*410T>A		3_prime_UTR	Exon 6 of 6	ENSP00000264468.6
	CD86	ENST00000469710.5	TSL:2	c.*410T>A		3_prime_UTR	Exon 6 of 6	ENSP00000418988.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 20058 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10076

African (AFR) AF: 0.00 AC: 0 AN: 168

American (AMR) AF: 0.00 AC: 0 AN: 1234

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 328

East Asian (EAS) AF: 0.00 AC: 0 AN: 344

South Asian (SAS) AF: 0.00 AC: 0 AN: 1284

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 804

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 60

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 14618

Other (OTH) AF: 0.00 AC: 0 AN: 1218

GnomAD4 genome Cov.: 24

Alfa AF: 0.00 Hom.: 7881

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.53
PhyloP100		-0.27

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: rs1915087; hg19: chr3-121838791;