Genetic Variant CCDC180:c.1789-951A>G (chr9-97329203-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020893.6(CCDC180):c.1789-951A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,156 control chromosomes in the GnomAD database, including 24,170 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 0.55 ( 24170 hom., cov: 33)

Consequence

CCDC180
NM_020893.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.200

Publications

7 publications found

Variant links:

Genes affected

CCDC180 (HGNC:29303): (coiled-coil domain containing 180) The protein encoded by this gene contains a coiled-coil domain. Alternative splicing results in multiple transcript variants encoding different isoforms. A single nucleotide polymorphism (SNP) in this gene has been associated with increased susceptibility to Behcet's Disease (PMID: 19442274). [provided by RefSeq, Dec 2016]

CCDC180 links:

SUGT1P4-STRA6LP-CCDC180 (HGNC:53835): (SUGT1P4-STRA6LP-CCDC180 readthrough) This locus represents a set of read-through transcripts spanning an upstream pseudogene (GeneID:100499484) extending into a downstream protein-coding locus (GeneID:100499483). All of the read-through transcripts are candidates for nonsense-mediated decay (NMD), so they are not thought to express a protein. [provided by RefSeq, Aug 2010]

SUGT1P4-STRA6LP-CCDC180 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020893.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC180	NM_020893.6	MANE Select	c.1789-951A>G	intron	N/A	NP_065944.3
CCDC180	NM_001348010.4		c.1780-951A>G	intron	N/A	NP_001334939.2
SUGT1P4-STRA6LP-CCDC180	NR_036527.1		n.3344-951A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC180	ENST00000529487.3	TSL:1 MANE Select	c.1789-951A>G	intron	N/A	ENSP00000434727.2
CCDC180	ENST00000494917.6	TSL:1	n.1992-951A>G	intron	N/A
SUGT1P4-STRA6LP-CCDC180	ENST00000375206.6	TSL:2	n.3273-951A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.547

AC:

83158

AN:

152038

Hom.:

24108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.726

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.614

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.576

Gnomad SAS

AF:

0.548

Gnomad FIN

AF:

0.363

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.526

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

GnomAD4 genome

AF:

0.547

AC:

83278

AN:

152156

Hom.:

24170

Cov.:

AF XY:

0.542

AC XY:

40338

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.727

AC:

30164

AN:

41512

American (AMR)

AF:

0.615

AC:

9399

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

1540

AN:

3466

East Asian (EAS)

AF:

0.577

AC:

2988

AN:

5178

South Asian (SAS)

AF:

0.549

AC:

2645

AN:

4822

European-Finnish (FIN)

AF:

0.363

AC:

3836

AN:

10574

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.458

AC:

31151

AN:

67998

Other (OTH)

AF:

0.523

AC:

1106

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1881

3761

5642

7522

9403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<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:

0.532

Hom.:

3946

Bravo

AF:

0.573

Asia WGS

AF:

0.543

AC:

1887

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.2

(source)

DANN

Benign

0.40

PhyloP100

-0.20

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over