NM_153033.5:c.493+18_493+21dupAGGA

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_153033.5(KCTD7):c.493+18_493+21dupAGGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,612,412 control chromosomes in the GnomAD database, including 13,706 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1236 hom., cov: 30)

Exomes 𝑓: 0.12 ( 12470 hom. )

Consequence

KCTD7
NM_153033.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -1.11

Publications

4 publications found

Variant links:

Genes affected

KCTD7 (HGNC:21957): (potassium channel tetramerization domain containing 7) This gene encodes a member of the potassium channel tetramerization domain-containing protein family. Family members are identified on a structural basis and contain an amino-terminal domain similar to the T1 domain present in the voltage-gated potassium channel. Mutations in this gene have been associated with progressive myoclonic epilepsy-3. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jan 2011]

KCTD7 Gene-Disease associations (from GenCC):

progressive myoclonic epilepsy type 3
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet
progressive myoclonus epilepsy
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen

KCTD7 links:

ENSG00000284461 (HGNC:):

ENSG00000284461 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 7-66638448-C-CAGGA is Benign according to our data. Variant chr7-66638448-C-CAGGA is described in ClinVar as Benign. ClinVar VariationId is 262690.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCTD7	NM_153033.5 link	c.493+18_493+21dupAGGA		intron_variant	Intron 3 of 3	ENST00000639828.2	NP_694578.1	Q96MP8-1A0A024RDN7
KCTD7	NM_001167961.2 link	c.493+18_493+21dupAGGA		intron_variant	Intron 3 of 4		NP_001161433.1	Q96MP8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCTD7	ENST00000639828.2 link	c.493+18_493+21dupAGGA		intron_variant	Intron 3 of 3	2	NM_153033.5	ENSP00000492240.1		Q96MP8-1
ENSG00000284461	ENST00000503687.2 link	n.323+18_323+21dupAGGA		intron_variant	Intron 2 of 12	2		ENSP00000421074.1		E9PHB8

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18092

AN:

151934

Hom.:

1230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0810

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.197

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.118

GnomAD2 exomes

AF:

0.132

AC:

32889

AN:

249990

AF XY:

0.131

show subpopulations

Gnomad AFR exome

AF:

0.0767

Gnomad AMR exome

AF:

0.101

Gnomad ASJ exome

AF:

0.217

Gnomad EAS exome

AF:

0.176

Gnomad FIN exome

AF:

0.232

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.124

AC:

180835

AN:

1460360

Hom.:

12470

Cov.:

AF XY:

0.124

AC XY:

90182

AN XY:

726232

show subpopulations

African (AFR)

AF:

0.0803

AC:

2684

AN:

33432

American (AMR)

AF:

0.101

AC:

4506

AN:

44684

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

5488

AN:

26114

East Asian (EAS)

AF:

0.268

AC:

10623

AN:

39650

South Asian (SAS)

AF:

0.124

AC:

10654

AN:

86226

European-Finnish (FIN)

AF:

0.232

AC:

12363

AN:

53394

Middle Eastern (MID)

AF:

0.111

AC:

640

AN:

5750

European-Non Finnish (NFE)

AF:

0.114

AC:

126409

AN:

1110784

Other (OTH)

AF:

0.124

AC:

7468

AN:

60326

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

8041

16082

24123

32164

40205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4754

9508

14262

19016

23770

<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:

0.119

AC:

18117

AN:

152052

Hom.:

1236

Cov.:

AF XY:

0.124

AC XY:

9242

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.0811

AC:

3364

AN:

41474

American (AMR)

AF:

0.107

AC:

1630

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

692

AN:

3470

East Asian (EAS)

AF:

0.196

AC:

1013

AN:

5158

South Asian (SAS)

AF:

0.120

AC:

579

AN:

4822

European-Finnish (FIN)

AF:

0.234

AC:

2466

AN:

10554

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.118

AC:

7993

AN:

67974

Other (OTH)

AF:

0.124

AC:

261

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

804

1608

2413

3217

4021

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

198

396

594

792

990

<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:

0.133

Hom.:

236

Bravo

AF:

0.108

Asia WGS

AF:

0.170

AC:

589

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 29, 2014

GeneDx

Significance:Benign

Review Status:flagged submission

Collection Method:clinical testing

The variant is found in EPILEPSY,INFANT-EPI panel(s). -

Progressive myoclonic epilepsy type 3

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Aug 19, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

Jan 29, 2016

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

May 16, 2017

Mayo Clinic Laboratories, Mayo Clinic

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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