Genetic Variant CCDC157:p.Asp51Asn (chr22-30366151-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001017437.5(CCDC157):c.151G>A(p.Asp51Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,613,584 control chromosomes in the GnomAD database, including 41,813 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 0.20 ( 3366 hom., cov: 32)

Exomes 𝑓: 0.22 ( 38447 hom. )

Consequence

CCDC157
NM_001017437.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 9.17

Publications

31 publications found

Variant links:

Genes affected

CCDC157 (HGNC:33854): (coiled-coil domain containing 157)

CCDC157 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=0.0016170144).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC157	NM_001017437.5 link	c.151G>A	p.Asp51Asn	missense_variant	Exon 3 of 12	ENST00000338306.8	NP_001017437.3	Q569K6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC157	ENST00000338306.8 link	c.151G>A	p.Asp51Asn	missense_variant	Exon 3 of 12	5	NM_001017437.5	ENSP00000343087.3		Q569K6

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

30703

AN:

152104

Hom.:

3366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.180

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.0960

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.247

GnomAD2 exomes

AF:

0.197

AC:

49350

AN:

250802

AF XY:

0.199

show subpopulations

Gnomad AFR exome

AF:

0.149

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.318

Gnomad EAS exome

AF:

0.143

Gnomad FIN exome

AF:

0.163

Gnomad NFE exome

AF:

0.246

Gnomad OTH exome

AF:

0.233

GnomAD4 exome

AF:

0.224

AC:

326929

AN:

1461362

Hom.:

38447

Cov.:

AF XY:

0.221

AC XY:

160937

AN XY:

727028

show subpopulations

African (AFR)

AF:

0.153

AC:

5121

AN:

33480

American (AMR)

AF:

0.147

AC:

6563

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.316

AC:

8267

AN:

26136

East Asian (EAS)

AF:

0.109

AC:

4332

AN:

39700

South Asian (SAS)

AF:

0.110

AC:

9522

AN:

86258

European-Finnish (FIN)

AF:

0.160

AC:

8463

AN:

52936

Middle Eastern (MID)

AF:

0.265

AC:

1528

AN:

5768

European-Non Finnish (NFE)

AF:

0.242

AC:

269422

AN:

1111974

Other (OTH)

AF:

0.227

AC:

13711

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

16387

32774

49162

65549

81936

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8988

17976

26964

35952

44940

<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:

0.202

AC:

30704

AN:

152222

Hom.:

3366

Cov.:

AF XY:

0.195

AC XY:

14509

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.153

AC:

6335

AN:

41532

American (AMR)

AF:

0.209

AC:

3192

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.320

AC:

1109

AN:

3466

East Asian (EAS)

AF:

0.135

AC:

696

AN:

5174

South Asian (SAS)

AF:

0.0955

AC:

461

AN:

4828

European-Finnish (FIN)

AF:

0.157

AC:

1662

AN:

10610

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.242

AC:

16465

AN:

68000

Other (OTH)

AF:

0.244

AC:

516

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1304

2608

3912

5216

6520

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.238

Hom.:

8501

Bravo

AF:

0.207

TwinsUK

AF:

0.234

AC:

866

ALSPAC

AF:

0.252

AC:

971

ESP6500AA

AF:

0.151

AC:

667

ESP6500EA

AF:

0.256

AC:

2204

ExAC

AF:

0.196

AC:

23796

Asia WGS

AF:

0.130

AC:

455

AN:

3478

EpiCase

AF:

0.265

EpiControl

AF:

0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.43

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.32

CADD

Pathogenic

(source)

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.10

T;T;T;T;.

Eigen

Pathogenic

0.78

Eigen_PC

Pathogenic

0.77

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.91

D;.;D;D;D

MetaRNN

Benign

0.0016

T;T;T;T;T

MetaSVM

Benign

-1.2

MutationAssessor

Uncertain

2.2

.;M;M;.;.

PhyloP100

9.2

PrimateAI

Uncertain

0.74

PROVEAN

Uncertain

-3.6

D;N;N;D;D

REVEL

Uncertain

0.35

Sift

Benign

0.11

T;T;T;T;T

Sift4G

Uncertain

0.045

D;D;D;D;D

Polyphen

1.0

.;D;D;.;.

Vest4

0.79

MPC

0.46

ClinPred

0.010

GERP RS

5.3

Varity_R

0.16

gMVP

0.45

Mutation Taster

=92/8

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