rs9282638

Positions:

• chr3-119544923-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005191.4(CD80):​c.101-56A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,411,842 control chromosomes in the GnomAD database, including 15,266 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 0.16 (2206 hom., cov: 32)
  • Exomes 𝑓: 0.14 (13060 hom.)
• Consequence: CD80 NM_005191.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD80	NM_005191.4	c.101-56A>G		intron_variant		ENST00000264246.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD80	ENST00000264246.8	c.101-56A>G		intron_variant		1	NM_005191.4	P2
CD80	ENST00000383669.3	c.101-56A>G		intron_variant		1		A2
CD80	ENST00000478182.5	c.101-56A>G		intron_variant		1		P2
CD80	ENST00000463729.1	n.213-56A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24377 AN: 152056 Hom.: 2204 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0628

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0536

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.146

GnomAD4 exome AF: 0.138 AC: 173342 AN: 1259668 Hom.: 13060 AF XY: 0.135 AC XY: 84113 AN XY: 625004

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.0799

Gnomad4 ASJ exome AF: 0.116

Gnomad4 EAS exome AF: 0.000349

Gnomad4 SAS exome AF: 0.0539

Gnomad4 FIN exome AF: 0.183

Gnomad4 NFE exome AF: 0.147

Gnomad4 OTH exome AF: 0.127

GnomAD4 genome AF: 0.160 AC: 24393 AN: 152174 Hom.: 2206 Cov.: 32 AF XY: 0.160 AC XY: 11922 AN XY: 74410

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0535

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.144

Alfa AF: 0.159 Hom.: 465

Bravo AF: 0.158

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.049
DANN	Benign	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

Publications

LitVar

Other links and lift over

dbSNP: rs9282638; hg19: chr3-119263770;