Genetic Variant NM_001394669.1:c.*71G>A (chr17-82101611-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_001394669.1(CCDC57):c.*71G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,273,680 control chromosomes in the GnomAD database, including 29,503 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 0.23 ( 4212 hom., cov: 34)

Exomes 𝑓: 0.21 ( 25291 hom. )

Consequence

CCDC57
NM_001394669.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.200

Publications

19 publications found

Variant links:

Genes affected

CCDC57 (HGNC:27564): (coiled-coil domain containing 57) Involved in several processes, including G2/M transition of mitotic cell cycle; cilium assembly; and microtubule cytoskeleton organization. Located in centriolar satellite; centriole; and spindle microtubule. [provided by Alliance of Genome Resources, Apr 2022]

CCDC57 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394669.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC57	NM_001394669.1	MANE Select	c.*71G>A	3_prime_UTR	Exon 19 of 19	NP_001381598.1
CCDC57	NM_001394670.1		c.*71G>A	3_prime_UTR	Exon 20 of 20	NP_001381599.1
CCDC57	NM_198082.4		c.*71G>A	3_prime_UTR	Exon 17 of 17	NP_932348.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCDC57	ENST00000694881.1	MANE Select	c.*71G>A	3_prime_UTR	Exon 19 of 19	ENSP00000511565.1
CCDC57	ENST00000665763.1		c.*71G>A	3_prime_UTR	Exon 20 of 20	ENSP00000499556.1
CCDC57	ENST00000875325.1		c.*71G>A	3_prime_UTR	Exon 20 of 20	ENSP00000545384.1

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34748

AN:

152072

Hom.:

4211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.0497

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.217

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.214

GnomAD4 exome

AF:

0.206

AC:

230513

AN:

1121490

Hom.:

25291

Cov.:

AF XY:

0.204

AC XY:

115776

AN XY:

566294

show subpopulations

African (AFR)

AF:

0.287

AC:

7083

AN:

24676

American (AMR)

AF:

0.117

AC:

3503

AN:

29978

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

2978

AN:

21916

East Asian (EAS)

AF:

0.0545

AC:

1999

AN:

36696

South Asian (SAS)

AF:

0.161

AC:

11351

AN:

70676

European-Finnish (FIN)

AF:

0.217

AC:

9630

AN:

44452

Middle Eastern (MID)

AF:

0.185

AC:

887

AN:

4786

European-Non Finnish (NFE)

AF:

0.219

AC:

183544

AN:

839338

Other (OTH)

AF:

0.195

AC:

9538

AN:

48972

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

8557

17113

25670

34226

42783

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5464

10928

16392

21856

27320

<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:

0.228

AC:

34763

AN:

152190

Hom.:

4212

Cov.:

AF XY:

0.224

AC XY:

16633

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.295

AC:

12229

AN:

41520

American (AMR)

AF:

0.165

AC:

2519

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.147

AC:

511

AN:

3468

East Asian (EAS)

AF:

0.0496

AC:

257

AN:

5178

South Asian (SAS)

AF:

0.151

AC:

730

AN:

4830

European-Finnish (FIN)

AF:

0.217

AC:

2295

AN:

10600

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.229

AC:

15591

AN:

67970

Other (OTH)

AF:

0.212

AC:

448

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

1342

2684

4027

5369

6711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.224

Hom.:

6053

Bravo

AF:

0.225

Asia WGS

AF:

0.109

AC:

378

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.3

(source)

DANN

Benign

0.50

PhyloP100

-0.20

PromoterAI

-0.052

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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