dbSNP rs3734805: CCDC170:c.*68A>C (chr6-151618215-A-C) – 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.*68A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 1,341,036 control chromosomes in the GnomAD database, including 5,350 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.073 ( 588 hom., cov: 32)

Exomes 𝑓: 0.079 ( 4762 hom. )

Consequence

CCDC170
NM_025059.4 3_prime_UTR

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.00500

Publications

58 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4 link	c.*68A>C	3_prime_UTR_variant	Exon 11 of 11	ENST00000239374.8	NP_079335.2	Q8IYT3
CCDC170	XM_011536147.3 link	c.*68A>C	3_prime_UTR_variant	Exon 11 of 11		XP_011534449.1
CCDC170	XM_011536148.3 link	c.*68A>C	3_prime_UTR_variant	Exon 10 of 10		XP_011534450.1
CCDC170	XM_047419372.1 link	c.*68A>C	3_prime_UTR_variant	Exon 10 of 10		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8 link	c.*68A>C		3_prime_UTR_variant	Exon 11 of 11	1	NM_025059.4	ENSP00000239374.6		Q8IYT3

Frequencies

GnomAD3 genomes

AF:

0.0727

AC:

11060

AN:

152116

Hom.:

589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0450

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.0709

Gnomad ASJ

AF:

0.0962

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.0673

Gnomad FIN

AF:

0.0263

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0782

Gnomad OTH

AF:

0.0924

GnomAD4 exome

AF:

0.0794

AC:

94405

AN:

1188802

Hom.:

4762

Cov.:

AF XY:

0.0791

AC XY:

47217

AN XY:

596630

show subpopulations

African (AFR)

AF:

0.0433

AC:

1191

AN:

27494

American (AMR)

AF:

0.0526

AC:

2103

AN:

39988

Ashkenazi Jewish (ASJ)

AF:

0.0969

AC:

2168

AN:

22378

East Asian (EAS)

AF:

0.265

AC:

10031

AN:

37892

South Asian (SAS)

AF:

0.0600

AC:

4497

AN:

74940

European-Finnish (FIN)

AF:

0.0312

AC:

1618

AN:

51846

Middle Eastern (MID)

AF:

0.107

AC:

406

AN:

3778

European-Non Finnish (NFE)

AF:

0.0771

AC:

67820

AN:

879648

Other (OTH)

AF:

0.0899

AC:

4571

AN:

50838

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

4141

8282

12423

16564

20705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2366

4732

7098

9464

11830

<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:

0.0726

AC:

11058

AN:

152234

Hom.:

588

Cov.:

AF XY:

0.0714

AC XY:

5313

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0450

AC:

1870

AN:

41550

American (AMR)

AF:

0.0708

AC:

1083

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0962

AC:

334

AN:

3472

East Asian (EAS)

AF:

0.305

AC:

1577

AN:

5168

South Asian (SAS)

AF:

0.0678

AC:

327

AN:

4826

European-Finnish (FIN)

AF:

0.0263

AC:

279

AN:

10594

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0782

AC:

5318

AN:

68014

Other (OTH)

AF:

0.0929

AC:

196

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

515

1029

1544

2058

2573

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0828

Hom.:

3014

Bravo

AF:

0.0767

Asia WGS

AF:

0.165

AC:

571

AN:

3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Estrogen resistance syndrome

Uncertain:1

Mar 01, 2014

Department of Breast and Endocrine Surgery, Kumamoto University

Significance:Uncertain significance

Review Status:no assertion criteria provided

Collection Method:research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.39

(source)

DANN

Benign

0.51

PhyloP100

-0.0050

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over