dbSNP rs9282638: CD80:c.101-56A>G (chr3-119544923-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45

Publications

11 publications found

Variant links:

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]

CD80 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_005191.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD80	NM_005191.4	MANE Select	c.101-56A>G		intron	N/A	NP_005182.1	P33681-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD80	ENST00000264246.8	TSL:1 MANE Select	c.101-56A>G	intron	N/A	ENSP00000264246.3	P33681-1
CD80	ENST00000478182.5	TSL:1	c.101-56A>G	intron	N/A	ENSP00000418364.1	P33681-1
CD80	ENST00000383669.3	TSL:1	c.101-56A>G	intron	N/A	ENSP00000373165.3	P33681-2

Frequencies

GnomAD3 genomes

AF:

0.160

AC:

24377

AN:

152056

Hom.:

2204

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.250

AC:

7187

AN:

28796

American (AMR)

AF:

0.0799

AC:

2698

AN:

33778

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

2511

AN:

21718

East Asian (EAS)

AF:

0.000349

AC:

AN:

37266

South Asian (SAS)

AF:

0.0539

AC:

3886

AN:

72104

European-Finnish (FIN)

AF:

0.183

AC:

9073

AN:

49714

Middle Eastern (MID)

AF:

0.102

AC:

533

AN:

5248

European-Non Finnish (NFE)

AF:

0.147

AC:

140700

AN:

958056

Other (OTH)

AF:

0.127

AC:

6741

AN:

52988

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

7331

14662

21992

29323

36654

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4974

9948

14922

19896

24870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.160

AC:

24393

AN:

152174

Hom.:

2206

Cov.:

AF XY:

0.160

AC XY:

11922

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.239

AC:

9927

AN:

41498

American (AMR)

AF:

0.106

AC:

1618

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.105

AC:

363

AN:

3470

East Asian (EAS)

AF:

0.00116

AC:

AN:

5186

South Asian (SAS)

AF:

0.0535

AC:

258

AN:

4824

European-Finnish (FIN)

AF:

0.189

AC:

2000

AN:

10592

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.145

AC:

9834

AN:

67998

Other (OTH)

AF:

0.144

AC:

304

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1051

2103

3154

4206

5257

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.162

Hom.:

483

Bravo

AF:

0.158

Asia WGS

AF:

0.0420

AC:

146

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.049

(source)

DANN

Benign

0.27

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over