rs2222631

Variant names:

• chr3-119553544-G-A
• rs2222631
• NM_005191.4:c.100+4085C>T

Variant summary

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

The NM_005191.4(CD80):​c.100+4085C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,020 control chromosomes in the GnomAD database, including 22,998 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 0.54 (22998 hom., cov: 32)
• Consequence: CD80 NM_005191.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457
• Publications: 14 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD80	NM_005191.4	c.100+4085C>T		intron_variant	Intron 2 of 6	ENST00000264246.8	NP_005182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD80	ENST00000264246.8	c.100+4085C>T		intron_variant	Intron 2 of 6	1	NM_005191.4	ENSP00000264246.3
CD80	ENST00000478182.5	c.100+4085C>T		intron_variant	Intron 2 of 5	1		ENSP00000418364.1
CD80	ENST00000383669.3	c.100+4085C>T		intron_variant	Intron 1 of 3	1		ENSP00000373165.3
CD80	ENST00000463729.1	n.212+4085C>T		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81990 AN: 151902 Hom.: 22943 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.540 AC: 82104 AN: 152020 Hom.: 22998 Cov.: 32 AF XY: 0.538 AC XY: 39970 AN XY: 74306

African (AFR) AF: 0.691 AC: 28636 AN: 41468

American (AMR) AF: 0.531 AC: 8124 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1584 AN: 3466

East Asian (EAS) AF: 0.520 AC: 2683 AN: 5156

South Asian (SAS) AF: 0.489 AC: 2356 AN: 4820

European-Finnish (FIN) AF: 0.449 AC: 4734 AN: 10550

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32080 AN: 67950

Other (OTH) AF: 0.530 AC: 1119 AN: 2112

Alfa AF: 0.484 Hom.: 28878

Bravo AF: 0.554

Asia WGS AF: 0.525 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.4
DANN	Benign	0.51
PhyloP100		0.46
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: rs2222631; hg19: chr3-119272391;