dbSNP rs3748841: CCDC30:p.Gln91His (chr1-42497129-A-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.273A>T(p.Gln91His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,232,682 control chromosomes in the GnomAD database, including 15,020 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/9 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 1550 hom., cov: 32)

Exomes 𝑓: 0.16 ( 13470 hom. )

Consequence

CCDC30
NM_001395517.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.360

Publications

4 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 (MetaRNN=0.002275467).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 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	HGVSp	Effect	Exon Rank	Protein	UniProt
CCDC30	NM_001395517.1	MANE Select	c.273A>T	p.Gln91His	missense	Exon 5 of 21	NP_001382446.1	A0A590UK19
CCDC30	NM_001395379.1		c.273A>T	p.Gln91His	missense	Exon 5 of 18	NP_001382308.1
CCDC30	NM_001395382.1		c.273A>T	p.Gln91His	missense	Exon 5 of 17	NP_001382311.1	A0A590UJA8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CCDC30	ENST00000657597.2	MANE Select	c.273A>T	p.Gln91His	missense	Exon 5 of 21	ENSP00000499662.2	A0A590UK19
CCDC30	ENST00000477155.6	TSL:1	n.*250A>T		non_coding_transcript_exon	Exon 6 of 23	ENSP00000421479.3	D6RFH8
CCDC30	ENST00000507855.5	TSL:1	n.333A>T		non_coding_transcript_exon	Exon 2 of 15

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20704

AN:

152112

Hom.:

1553

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0900

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.184

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.156

GnomAD4 exome

AF:

0.157

AC:

169430

AN:

1080452

Hom.:

13470

Cov.:

AF XY:

0.156

AC XY:

79746

AN XY:

510128

show subpopulations

African (AFR)

AF:

0.0888

AC:

2044

AN:

23028

American (AMR)

AF:

0.158

AC:

1331

AN:

8424

Ashkenazi Jewish (ASJ)

AF:

0.197

AC:

2830

AN:

14378

East Asian (EAS)

AF:

0.167

AC:

4430

AN:

26508

South Asian (SAS)

AF:

0.115

AC:

2249

AN:

19572

European-Finnish (FIN)

AF:

0.113

AC:

2432

AN:

21526

Middle Eastern (MID)

AF:

0.150

AC:

684

AN:

4546

European-Non Finnish (NFE)

AF:

0.160

AC:

146532

AN:

918648

Other (OTH)

AF:

0.157

AC:

6898

AN:

43822

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

6720

13440

20161

26881

33601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6024

12048

18072

24096

30120

<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:

0.136

AC:

20705

AN:

152230

Hom.:

1550

Cov.:

AF XY:

0.133

AC XY:

9896

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0900

AC:

3739

AN:

41530

American (AMR)

AF:

0.155

AC:

2368

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

730

AN:

3472

East Asian (EAS)

AF:

0.184

AC:

953

AN:

5176

South Asian (SAS)

AF:

0.115

AC:

554

AN:

4830

European-Finnish (FIN)

AF:

0.106

AC:

1124

AN:

10604

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10791

AN:

68014

Other (OTH)

AF:

0.155

AC:

328

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

904

1808

2712

3616

4520

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.147

Hom.:

247

Bravo

AF:

0.143

TwinsUK

AF:

0.160

AC:

594

ALSPAC

AF:

0.165

AC:

636

Asia WGS

AF:

0.139

AC:

481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_noAF

Benign

-0.41

CADD

Benign

7.5

(source)

DANN

Benign

0.78

FATHMM_MKL

Benign

0.054

LIST_S2

Benign

0.29

MetaRNN

Benign

0.0023

PhyloP100

-0.36

GERP RS

-1.9

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over