dbSNP rs2302706: KCTD10:p.Val206Val (chr12-109456223-A-G) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_031954.5(KCTD10):c.618T>C(p.Val206Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,613,982 control chromosomes in the GnomAD database, including 24,822 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 0.17 ( 2240 hom., cov: 32)

Exomes 𝑓: 0.17 ( 22582 hom. )

Consequence

KCTD10
NM_031954.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0460

Publications

30 publications found

Variant links:

Genes affected

KCTD10 (HGNC:23236): (potassium channel tetramerization domain containing 10) The protein encoded by this gene binds proliferating cell nuclear antigen (PCNA) and may be involved in DNA synthesis and cell proliferation. In addition, the encoded protein may be a tumor suppressor. Several protein-coding and non-protein coding transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]

KCTD10 Gene-Disease associations (from GenCC):

multiple congenital anomalies/dysmorphic syndrome
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

KCTD10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.039).

BP7

Synonymous conserved (PhyloP=0.046 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCTD10	NM_031954.5 link	c.618T>C	p.Val206Val	synonymous_variant	Exon 6 of 7	ENST00000228495.11	NP_114160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCTD10	ENST00000228495.11 link	c.618T>C	p.Val206Val	synonymous_variant	Exon 6 of 7	1	NM_031954.5	ENSP00000228495.6

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25769

AN:

152056

Hom.:

2244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.0989

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.177

Gnomad OTH

AF:

0.173

GnomAD2 exomes

AF:

0.161

AC:

40607

AN:

251486

AF XY:

0.162

show subpopulations

Gnomad AFR exome

AF:

0.186

Gnomad AMR exome

AF:

0.145

Gnomad ASJ exome

AF:

0.185

Gnomad EAS exome

AF:

0.146

Gnomad FIN exome

AF:

0.104

Gnomad NFE exome

AF:

0.178

Gnomad OTH exome

AF:

0.168

GnomAD4 exome

AF:

0.174

AC:

254222

AN:

1461806

Hom.:

22582

Cov.:

AF XY:

0.172

AC XY:

125332

AN XY:

727216

show subpopulations

African (AFR)

AF:

0.181

AC:

6055

AN:

33480

American (AMR)

AF:

0.146

AC:

6520

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

4995

AN:

26136

East Asian (EAS)

AF:

0.155

AC:

6167

AN:

39700

South Asian (SAS)

AF:

0.142

AC:

12213

AN:

86256

European-Finnish (FIN)

AF:

0.108

AC:

5745

AN:

53420

Middle Eastern (MID)

AF:

0.193

AC:

1114

AN:

5768

European-Non Finnish (NFE)

AF:

0.181

AC:

201012

AN:

1111926

Other (OTH)

AF:

0.172

AC:

10401

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

12076

24153

36229

48306

60382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7090

14180

21270

28360

35450

<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:

0.169

AC:

25776

AN:

152176

Hom.:

2240

Cov.:

AF XY:

0.164

AC XY:

12194

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.184

AC:

7644

AN:

41514

American (AMR)

AF:

0.158

AC:

2419

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

669

AN:

3470

East Asian (EAS)

AF:

0.137

AC:

709

AN:

5168

South Asian (SAS)

AF:

0.134

AC:

644

AN:

4822

European-Finnish (FIN)

AF:

0.0989

AC:

1048

AN:

10596

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.177

AC:

12024

AN:

67994

Other (OTH)

AF:

0.176

AC:

372

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1106

2212

3317

4423

5529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<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:

0.180

Hom.:

3967

Bravo

AF:

0.176

Asia WGS

AF:

0.150

AC:

521

AN:

3478

EpiCase

AF:

0.185

EpiControl

AF:

0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

7.4

(source)

DANN

Benign

0.65

PhyloP100

0.046

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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