Genetic Variant CCDC80:c.1878+105A>G (chr3-112637923-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_199511.3(CCDC80):c.1878+105A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 1,502,414 control chromosomes in the GnomAD database, including 368,975 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 0.68 ( 35893 hom., cov: 32)

Exomes 𝑓: 0.70 ( 333082 hom. )

Consequence

CCDC80
NM_199511.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0140

Publications

9 publications found

Variant links:

Genes affected

CCDC80 (HGNC:30649): (coiled-coil domain containing 80) Predicted to enable glycosaminoglycan binding activity. Predicted to act upstream of or within extracellular matrix organization; positive regulation of cell-substrate adhesion; and response to bacterium. Predicted to be located in extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

CCDC80 links:

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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=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCDC80	NM_199511.3 link	c.1878+105A>G	intron_variant	Intron 2 of 7	ENST00000206423.8	NP_955805.1	Q76M96-1
CCDC80	NM_199512.3 link	c.1878+105A>G	intron_variant	Intron 2 of 7		NP_955806.1	Q76M96-1
CCDC80	XM_047447495.1 link	c.1911+105A>G	intron_variant	Intron 1 of 6		XP_047303451.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCDC80	ENST00000206423.8 link	c.1878+105A>G	intron_variant	Intron 2 of 7	1	NM_199511.3	ENSP00000206423.3	Q76M96-1
CCDC80	ENST00000439685.6 link	c.1878+105A>G	intron_variant	Intron 2 of 7	1		ENSP00000411814.2	Q76M96-1
CCDC80	ENST00000461431.1 link	c.69+105A>G	intron_variant	Intron 1 of 5	3		ENSP00000420123.1	H7C5K4

Frequencies

GnomAD3 genomes

AF:

0.684

AC:

103996

AN:

151930

Hom.:

35865

Cov.:

show subpopulations

Gnomad AFR

AF:

0.615

Gnomad AMI

AF:

0.678

Gnomad AMR

AF:

0.688

Gnomad ASJ

AF:

0.702

Gnomad EAS

AF:

0.860

Gnomad SAS

AF:

0.784

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.697

Gnomad OTH

AF:

0.630

GnomAD4 exome

AF:

0.701

AC:

946581

AN:

1350364

Hom.:

333082

AF XY:

0.703

AC XY:

466293

AN XY:

663516

show subpopulations

African (AFR)

AF:

0.607

AC:

18208

AN:

30008

American (AMR)

AF:

0.747

AC:

20381

AN:

27274

Ashkenazi Jewish (ASJ)

AF:

0.699

AC:

13817

AN:

19764

East Asian (EAS)

AF:

0.869

AC:

33870

AN:

38982

South Asian (SAS)

AF:

0.779

AC:

52505

AN:

67382

European-Finnish (FIN)

AF:

0.747

AC:

30578

AN:

40912

Middle Eastern (MID)

AF:

0.634

AC:

3161

AN:

4986

European-Non Finnish (NFE)

AF:

0.690

AC:

734767

AN:

1064990

Other (OTH)

AF:

0.701

AC:

39294

AN:

56066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

14083

28166

42250

56333

70416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19332

38664

57996

77328

96660

<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:

0.684

AC:

104077

AN:

152050

Hom.:

35893

Cov.:

AF XY:

0.689

AC XY:

51230

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.615

AC:

25507

AN:

41444

American (AMR)

AF:

0.688

AC:

10518

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.702

AC:

2436

AN:

3472

East Asian (EAS)

AF:

0.860

AC:

4438

AN:

5160

South Asian (SAS)

AF:

0.785

AC:

3783

AN:

4822

European-Finnish (FIN)

AF:

0.749

AC:

7923

AN:

10578

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.697

AC:

47359

AN:

67978

Other (OTH)

AF:

0.629

AC:

1330

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1670

3341

5011

6682

8352

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

822

1644

2466

3288

4110

<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:

0.696

Hom.:

32635

Bravo

AF:

0.674

Asia WGS

AF:

0.790

AC:

2747

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

6.9

(source)

DANN

Benign

0.85

PhyloP100

-0.014

PromoterAI

-0.013

Neutral

(source)

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