Genetic Variant NM_025059.4:c.1294-129G>A (chr6-151592978-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_025059.4(CCDC170):c.1294-129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 963,046 control chromosomes in the GnomAD database, including 3,572 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 0.064 ( 450 hom., cov: 32)

Exomes 𝑓: 0.078 ( 3122 hom. )

Consequence

CCDC170
NM_025059.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.30

Publications

97 publications found

Variant links:

Genes affected

CCDC170 (HGNC:21177): (coiled-coil domain containing 170) The function of this gene and its encoded protein is not known. Several genome-wide association studies have implicated the region around this gene to be involved in breast cancer and bone mineral density, but no link to this specific gene has been found. [provided by RefSeq, May 2010]

CCDC170 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025059.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	NM_025059.4	MANE Select	c.1294-129G>A		intron	N/A	NP_079335.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	ENST00000239374.8	TSL:1 MANE Select	c.1294-129G>A		intron	N/A	ENSP00000239374.6
	CCDC170	ENST00000537358.1	TSL:3	n.-50G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.0641

AC:

9751

AN:

152146

Hom.:

449

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0314

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.0615

Gnomad ASJ

AF:

0.0774

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.0640

Gnomad FIN

AF:

0.0300

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0736

Gnomad OTH

AF:

0.0860

GnomAD4 exome

AF:

0.0775

AC:

62839

AN:

810782

Hom.:

3122

Cov.:

AF XY:

0.0776

AC XY:

32031

AN XY:

412778

show subpopulations

African (AFR)

AF:

0.0328

AC:

642

AN:

19588

American (AMR)

AF:

0.0487

AC:

1407

AN:

28914

Ashkenazi Jewish (ASJ)

AF:

0.0809

AC:

1435

AN:

17740

East Asian (EAS)

AF:

0.235

AC:

7701

AN:

32794

South Asian (SAS)

AF:

0.0593

AC:

3408

AN:

57484

European-Finnish (FIN)

AF:

0.0340

AC:

1297

AN:

38136

Middle Eastern (MID)

AF:

0.0826

AC:

237

AN:

2870

European-Non Finnish (NFE)

AF:

0.0756

AC:

43480

AN:

575196

Other (OTH)

AF:

0.0849

AC:

3232

AN:

38060

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2910

5820

8730

11640

14550

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1266

2532

3798

5064

6330

<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:

0.0641

AC:

9753

AN:

152264

Hom.:

450

Cov.:

AF XY:

0.0629

AC XY:

4681

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0314

AC:

1303

AN:

41552

American (AMR)

AF:

0.0615

AC:

940

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0774

AC:

268

AN:

3462

East Asian (EAS)

AF:

0.262

AC:

1354

AN:

5176

South Asian (SAS)

AF:

0.0649

AC:

313

AN:

4826

European-Finnish (FIN)

AF:

0.0300

AC:

318

AN:

10610

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0736

AC:

5007

AN:

68022

Other (OTH)

AF:

0.0879

AC:

186

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

467

935

1402

1870

2337

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0765

Hom.:

2504

Bravo

AF:

0.0673

Asia WGS

AF:

0.148

AC:

514

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.014

(source)

DANN

Benign

0.24

PhyloP100

-3.3

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