rs2061634

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020893.6(CCDC180):c.2435C>G(p.Ser812Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,612,734 control chromosomes in the GnomAD database, including 58,719 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7274 hom., cov: 32)

Exomes 𝑓: 0.26 ( 51445 hom. )

Consequence

CCDC180
NM_020893.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.620

Publications

35 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0012887716).

BP6

Variant 9-97343500-C-G is Benign according to our data. Variant chr9-97343500-C-G is described in ClinVar as Benign. ClinVar VariationId is 1268803.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 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	HGVSp	Effect	Exon Rank	Protein	UniProt
CCDC180	NM_020893.6	MANE Select	c.2435C>G	p.Ser812Cys	missense	Exon 19 of 37	NP_065944.3	A0A6E1Y6F7
CCDC180	NM_001348010.4		c.2426C>G	p.Ser809Cys	missense	Exon 20 of 21	NP_001334939.2
SUGT1P4-STRA6LP-CCDC180	NR_036527.1		n.3990C>G		non_coding_transcript_exon	Exon 33 of 49

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CCDC180	ENST00000529487.3	TSL:1 MANE Select	c.2435C>G	p.Ser812Cys	missense	Exon 19 of 37	ENSP00000434727.2	A0A6E1Y6F7
CCDC180	ENST00000494917.6	TSL:1	n.2638C>G		non_coding_transcript_exon	Exon 20 of 20
CCDC180	ENST00000867263.1		c.2435C>G	p.Ser812Cys	missense	Exon 20 of 35	ENSP00000537322.1

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44827

AN:

151876

Hom.:

7265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.415

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.290

GnomAD2 exomes

AF:

0.266

AC:

66801

AN:

251382

AF XY:

0.265

show subpopulations

Gnomad AFR exome

AF:

0.413

Gnomad AMR exome

AF:

0.296

Gnomad ASJ exome

AF:

0.324

Gnomad EAS exome

AF:

0.185

Gnomad FIN exome

AF:

0.145

Gnomad NFE exome

AF:

0.263

Gnomad OTH exome

AF:

0.265

GnomAD4 exome

AF:

0.261

AC:

381048

AN:

1460740

Hom.:

51445

Cov.:

AF XY:

0.262

AC XY:

190058

AN XY:

726740

show subpopulations

African (AFR)

AF:

0.420

AC:

14035

AN:

33442

American (AMR)

AF:

0.301

AC:

13460

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

8404

AN:

26122

East Asian (EAS)

AF:

0.162

AC:

6444

AN:

39694

South Asian (SAS)

AF:

0.278

AC:

23977

AN:

86232

European-Finnish (FIN)

AF:

0.153

AC:

8149

AN:

53394

Middle Eastern (MID)

AF:

0.346

AC:

1994

AN:

5766

European-Non Finnish (NFE)

AF:

0.259

AC:

287768

AN:

1111002

Other (OTH)

AF:

0.279

AC:

16817

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

14407

28814

43222

57629

72036

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9826

19652

29478

39304

49130

<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:

0.295

AC:

44876

AN:

151994

Hom.:

7274

Cov.:

AF XY:

0.288

AC XY:

21388

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.415

AC:

17184

AN:

41414

American (AMR)

AF:

0.294

AC:

4490

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

1142

AN:

3468

East Asian (EAS)

AF:

0.183

AC:

948

AN:

5174

South Asian (SAS)

AF:

0.267

AC:

1286

AN:

4808

European-Finnish (FIN)

AF:

0.141

AC:

1495

AN:

10576

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.257

AC:

17445

AN:

67962

Other (OTH)

AF:

0.289

AC:

610

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1565

3130

4696

6261

7826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

452

904

1356

1808

2260

<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:

0.265

Hom.:

4203

Bravo

AF:

0.312

TwinsUK

AF:

0.257

AC:

952

ALSPAC

AF:

0.255

AC:

982

ESP6500AA

AF:

0.419

AC:

1846

ESP6500EA

AF:

0.273

AC:

2349

ExAC

AF:

0.269

AC:

32615

Asia WGS

AF:

0.216

AC:

750

AN:

3478

EpiCase

AF:

0.276

EpiControl

AF:

0.271

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.96

Eigen

Benign

-0.84

Eigen_PC

Benign

-0.84

FATHMM_MKL

Benign

0.040

LIST_S2

Benign

0.33

MetaRNN

Benign

0.0013

MetaSVM

Benign

-0.91

PhyloP100

0.62

PrimateAI

Benign

0.30

PROVEAN

Benign

-1.3

REVEL

Benign

0.038

Sift

Benign

0.088

Sift4G

Uncertain

0.0070

Vest4

0.099

ClinPred

0.0079

GERP RS

1.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.067

gMVP

0.051

Mutation Taster

=93/7

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over