Genetic Variant NM_005191.4: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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD80	NM_005191.4 link	c.101-56A>G		intron_variant	Intron 2 of 6	ENST00000264246.8	NP_005182.1	P33681-1A0N0P2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CD80	ENST00000264246.8 link	c.101-56A>G	intron_variant	Intron 2 of 6	1	NM_005191.4	ENSP00000264246.3	P33681-1
CD80	ENST00000478182.5 link	c.101-56A>G	intron_variant	Intron 2 of 5	1		ENSP00000418364.1	P33681-1
CD80	ENST00000383669.3 link	c.101-56A>G	intron_variant	Intron 1 of 3	1		ENSP00000373165.3	P33681-2
CD80	ENST00000463729.1 link	n.213-56A>G	intron_variant	Intron 1 of 1	1

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 v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over