dbSNP rs12038786: CCDC30:c.891-17C>T (chr1-42556139-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001395517.1(CCDC30):c.891-17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,595,526 control chromosomes in the GnomAD database, including 116,354 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 0.38 ( 11449 hom., cov: 32)

Exomes 𝑓: 0.38 ( 104905 hom. )

Consequence

CCDC30
NM_001395517.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.259

Publications

11 publications found

Variant links:

Genes affected

CCDC30 (HGNC:26103): (coiled-coil domain containing 30)

CCDC30 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395517.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCDC30	NM_001395517.1	MANE Select	c.891-17C>T	intron	N/A	NP_001382446.1	A0A590UK19
CCDC30	NM_001080850.4		c.426-17C>T	intron	N/A	NP_001074319.1	Q5VVM6-1
CCDC30	NM_001395379.1		c.583-10157C>T	intron	N/A	NP_001382308.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCDC30	ENST00000657597.2	MANE Select	c.891-17C>T	intron	N/A	ENSP00000499662.2	A0A590UK19
CCDC30	ENST00000514642.1	TSL:1	c.28-10157C>T	intron	N/A	ENSP00000499505.1	A0A590UJL6
CCDC30	ENST00000477155.6	TSL:1	n.*831-17C>T	intron	N/A	ENSP00000421479.3	D6RFH8

Frequencies

GnomAD3 genomes

AF:

0.380

AC:

57625

AN:

151664

Hom.:

11435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.342

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.381

Gnomad EAS

AF:

0.593

Gnomad SAS

AF:

0.541

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.360

Gnomad OTH

AF:

0.386

GnomAD2 exomes

AF:

0.385

AC:

90716

AN:

235504

AF XY:

0.394

show subpopulations

Gnomad AFR exome

AF:

0.417

Gnomad AMR exome

AF:

0.305

Gnomad ASJ exome

AF:

0.382

Gnomad EAS exome

AF:

0.611

Gnomad FIN exome

AF:

0.241

Gnomad NFE exome

AF:

0.357

Gnomad OTH exome

AF:

0.369

GnomAD4 exome

AF:

0.376

AC:

542247

AN:

1443746

Hom.:

104905

Cov.:

AF XY:

0.380

AC XY:

272978

AN XY:

718088

show subpopulations

African (AFR)

AF:

0.419

AC:

13435

AN:

32052

American (AMR)

AF:

0.309

AC:

12531

AN:

40614

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

9571

AN:

25202

East Asian (EAS)

AF:

0.536

AC:

21197

AN:

39568

South Asian (SAS)

AF:

0.537

AC:

44535

AN:

82962

European-Finnish (FIN)

AF:

0.250

AC:

13253

AN:

53014

Middle Eastern (MID)

AF:

0.418

AC:

2362

AN:

5648

European-Non Finnish (NFE)

AF:

0.363

AC:

401692

AN:

1105216

Other (OTH)

AF:

0.398

AC:

23671

AN:

59470

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

15375

30750

46126

61501

76876

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13054

26108

39162

52216

65270

<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:

0.380

AC:

57686

AN:

151780

Hom.:

11449

Cov.:

AF XY:

0.379

AC XY:

28128

AN XY:

74154

show subpopulations

African (AFR)

AF:

0.416

AC:

17185

AN:

41322

American (AMR)

AF:

0.338

AC:

5162

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.381

AC:

1321

AN:

3470

East Asian (EAS)

AF:

0.593

AC:

3071

AN:

5182

South Asian (SAS)

AF:

0.540

AC:

2604

AN:

4820

European-Finnish (FIN)

AF:

0.253

AC:

2658

AN:

10486

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.360

AC:

24436

AN:

67926

Other (OTH)

AF:

0.391

AC:

824

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1812

3624

5437

7249

9061

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

572

1144

1716

2288

2860

<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:

0.368

Hom.:

2443

Bravo

AF:

0.388

Asia WGS

AF:

0.581

AC:

2020

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.8

(source)

DANN

Benign

0.50

PhyloP100

0.26

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over