dbSNP rs3734803: CCDC170:c.774+21G>A (chr6-151548510-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.774+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,506,348 control chromosomes in the GnomAD database, including 23,435 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 0.14 ( 1701 hom., cov: 32)

Exomes 𝑓: 0.18 ( 21734 hom. )

Consequence

CCDC170
NM_025059.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.62

Publications

9 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=-0.49).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4 link	c.774+21G>A	intron_variant	Intron 5 of 10	ENST00000239374.8	NP_079335.2	Q8IYT3
CCDC170	XM_011536147.3 link	c.792+21G>A	intron_variant	Intron 5 of 10		XP_011534449.1
CCDC170	XM_011536148.3 link	c.792+21G>A	intron_variant	Intron 5 of 9		XP_011534450.1
CCDC170	XM_047419372.1 link	c.774+21G>A	intron_variant	Intron 5 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8 link	c.774+21G>A		intron_variant	Intron 5 of 10	1	NM_025059.4	ENSP00000239374.6		Q8IYT3

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21645

AN:

151842

Hom.:

1698

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0855

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.272

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.163

GnomAD2 exomes

AF:

0.168

AC:

34084

AN:

203220

AF XY:

0.171

show subpopulations

Gnomad AFR exome

AF:

0.0845

Gnomad AMR exome

AF:

0.130

Gnomad ASJ exome

AF:

0.172

Gnomad EAS exome

AF:

0.271

Gnomad FIN exome

AF:

0.119

Gnomad NFE exome

AF:

0.177

Gnomad OTH exome

AF:

0.166

GnomAD4 exome

AF:

0.177

AC:

239600

AN:

1354388

Hom.:

21734

Cov.:

AF XY:

0.178

AC XY:

118890

AN XY:

666456

show subpopulations

African (AFR)

AF:

0.0852

AC:

2588

AN:

30384

American (AMR)

AF:

0.125

AC:

3994

AN:

31924

Ashkenazi Jewish (ASJ)

AF:

0.160

AC:

3468

AN:

21666

East Asian (EAS)

AF:

0.250

AC:

9686

AN:

38712

South Asian (SAS)

AF:

0.195

AC:

13184

AN:

67500

European-Finnish (FIN)

AF:

0.121

AC:

5977

AN:

49494

Middle Eastern (MID)

AF:

0.178

AC:

943

AN:

5290

European-Non Finnish (NFE)

AF:

0.180

AC:

190086

AN:

1054296

Other (OTH)

AF:

0.176

AC:

9674

AN:

55122

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

8515

17031

25546

34062

42577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6990

13980

20970

27960

34950

<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:

0.143

AC:

21659

AN:

151960

Hom.:

1701

Cov.:

AF XY:

0.142

AC XY:

10540

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.0854

AC:

3540

AN:

41456

American (AMR)

AF:

0.143

AC:

2180

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

543

AN:

3462

East Asian (EAS)

AF:

0.272

AC:

1398

AN:

5144

South Asian (SAS)

AF:

0.174

AC:

839

AN:

4818

European-Finnish (FIN)

AF:

0.107

AC:

1128

AN:

10556

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.169

AC:

11505

AN:

67944

Other (OTH)

AF:

0.169

AC:

358

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

926

1852

2778

3704

4630

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.164

Hom.:

3836

Bravo

AF:

0.143

Asia WGS

AF:

0.213

AC:

739

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

6.1

(source)

DANN

Benign

0.77

PhyloP100

1.6

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