rs6804441

Variant names:

• chr3-119542097-A-G
• rs6804441
• NM_005191.4:c.418+2453T>C

Variant summary

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

The NM_005191.4(CD80):​c.418+2453T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 122,986 control chromosomes in the GnomAD database, including 1,788 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 (1788 hom., cov: 21)
• Consequence: CD80 NM_005191.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 35 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005191.4. 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
	CD80	NM_005191.4	MANE Select	c.418+2453T>C		intron	N/A	NP_005182.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD80	ENST00000264246.8	TSL:1 MANE Select	c.418+2453T>C		intron	N/A	ENSP00000264246.3
	CD80	ENST00000478182.5	TSL:1	c.418+2453T>C		intron	N/A	ENSP00000418364.1
	CD80	ENST00000383669.3	TSL:1	c.418+2453T>C		intron	N/A	ENSP00000373165.3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 21277 AN: 122938 Hom.: 1791 Cov.: 21

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.173 AC: 21272 AN: 122986 Hom.: 1788 Cov.: 21 AF XY: 0.174 AC XY: 9992 AN XY: 57450

African (AFR) AF: 0.135 AC: 4235 AN: 31480

American (AMR) AF: 0.173 AC: 1717 AN: 9946

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 457 AN: 3238

East Asian (EAS) AF: 0.370 AC: 1502 AN: 4064

South Asian (SAS) AF: 0.232 AC: 800 AN: 3444

European-Finnish (FIN) AF: 0.146 AC: 828 AN: 5676

Middle Eastern (MID) AF: 0.289 AC: 55 AN: 190

European-Non Finnish (NFE) AF: 0.180 AC: 11204 AN: 62408

Other (OTH) AF: 0.171 AC: 291 AN: 1702

Alfa AF: 0.169 Hom.: 9643

Bravo AF: 0.154

Asia WGS AF: 0.245 AC: 848 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		0.18
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: rs6804441; hg19: chr3-119260944;