3-119569567-A-C

Variant names:

• chr3-119569567-A-C
• rs59374417
• ENST00000853991.1:c.-625T>G

Variant summary

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

The ENST00000853991.1(CD80):​c.-625T>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 144,914 control chromosomes in the GnomAD database, including 2,528 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 0.17 (2528 hom., cov: 30)
• Consequence: CD80 ENST00000853991.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 28 publications found

Genes affected

CD80 (HGNC:1700): (CD80 molecule) The protein encoded by this gene is a membrane receptor that is activated by the binding of CD28 or CTLA-4. The activated protein induces T-cell proliferation and cytokine production. This protein can act as a receptor for adenovirus subgroup B and may play a role in lupus neuropathy. [provided by RefSeq, Aug 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 (SAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000853991.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD80	ENST00000853991.1		c.-625T>G		upstream_gene	N/A	ENSP00000524050.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 25287 AN: 144814 Hom.: 2530 Cov.: 30

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.175 AC: 25301 AN: 144914 Hom.: 2528 Cov.: 30 AF XY: 0.176 AC XY: 12334 AN XY: 69996

African (AFR) AF: 0.268 AC: 10390 AN: 38830

American (AMR) AF: 0.149 AC: 2112 AN: 14188

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 664 AN: 3440

East Asian (EAS) AF: 0.257 AC: 1243 AN: 4840

South Asian (SAS) AF: 0.281 AC: 1286 AN: 4582

European-Finnish (FIN) AF: 0.119 AC: 1062 AN: 8910

Middle Eastern (MID) AF: 0.243 AC: 70 AN: 288

European-Non Finnish (NFE) AF: 0.120 AC: 8007 AN: 66914

Other (OTH) AF: 0.185 AC: 375 AN: 2028

Alfa AF: 0.130 Hom.: 2499

Bravo AF: 0.172

Asia WGS AF: 0.246 AC: 853 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.64
PhyloP100		0.035

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs59374417; hg19: chr3-119288414;