dbSNP rs3757318: CCDC170: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:

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=-0.92).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4 link	c.1294-129G>A	intron_variant	Intron 7 of 10	ENST00000239374.8	NP_079335.2	Q8IYT3
CCDC170	XM_011536147.3 link	c.1312-129G>A	intron_variant	Intron 7 of 10		XP_011534449.1
CCDC170	XM_011536148.3 link	c.1111-129G>A	intron_variant	Intron 6 of 9		XP_011534450.1
CCDC170	XM_047419372.1 link	c.1093-129G>A	intron_variant	Intron 6 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8 link	c.1294-129G>A		intron_variant	Intron 7 of 10	1	NM_025059.4	ENSP00000239374.6		Q8IYT3
CCDC170	ENST00000537358.1 link	n.-50G>A		upstream_gene_variant		3

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over