rs13071247

Positions:

• chr3-119547946-A-C

Variant summary

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

The NM_005191.4(CD80):​c.101-3079T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,852 control chromosomes in the GnomAD database, including 1,535 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 0.14 (1535 hom., cov: 32)
• Consequence: CD80 NM_005191.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD80	NM_005191.4	c.101-3079T>G		intron_variant		ENST00000264246.8	NP_005182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD80	ENST00000264246.8	c.101-3079T>G		intron_variant		1	NM_005191.4	ENSP00000264246	P2
CD80	ENST00000383669.3	c.101-3079T>G		intron_variant		1		ENSP00000373165	A2
CD80	ENST00000478182.5	c.101-3079T>G		intron_variant		1		ENSP00000418364	P2
CD80	ENST00000463729.1	n.213-3079T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20843 AN: 151736 Hom.: 1531 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.137 AC: 20869 AN: 151852 Hom.: 1535 Cov.: 32 AF XY: 0.137 AC XY: 10194 AN XY: 74192

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0601

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.123

Alfa AF: 0.152 Hom.: 271

Bravo AF: 0.131

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.77

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: rs13071247; hg19: chr3-119266793;