chr7-66628895-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_153033.5(KCTD7):​c.-170G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 530,728 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000026 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

KCTD7
NM_153033.5 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.490

Publications

1 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

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCTD7NM_153033.5 linkc.-170G>C 5_prime_UTR_variant Exon 1 of 4 ENST00000639828.2 NP_694578.1 Q96MP8-1A0A024RDN7
KCTD7NM_001167961.2 linkc.-170G>C 5_prime_UTR_variant Exon 1 of 5 NP_001161433.1 Q96MP8-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCTD7ENST00000639828.2 linkc.-170G>C 5_prime_UTR_variant Exon 1 of 4 2 NM_153033.5 ENSP00000492240.1 Q96MP8-1
ENSG00000284461ENST00000503687.2 linkn.-170G>C upstream_gene_variant 2 ENSP00000421074.1 E9PHB8

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152048
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000185
AC:
7
AN:
378680
Hom.:
0
Cov.:
5
AF XY:
0.0000103
AC XY:
2
AN XY:
194540
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
8106
American (AMR)
AF:
0.00
AC:
0
AN:
6542
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
9094
East Asian (EAS)
AF:
0.0000999
AC:
2
AN:
20028
South Asian (SAS)
AF:
0.00
AC:
0
AN:
18074
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
23390
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1478
European-Non Finnish (NFE)
AF:
0.0000184
AC:
5
AN:
271856
Other (OTH)
AF:
0.00
AC:
0
AN:
20112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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:
0.0000263
AC:
4
AN:
152048
Hom.:
0
Cov.:
30
AF XY:
0.0000135
AC XY:
1
AN XY:
74260
show subpopulations
African (AFR)
AF:
0.0000242
AC:
1
AN:
41406
American (AMR)
AF:
0.00
AC:
0
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3466
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5168
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4836
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10598
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
0.0000441
AC:
3
AN:
67986
Other (OTH)
AF:
0.00
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.513
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.00
Hom.:
0
Bravo
AF:
0.0000189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
0.91
DANN
Benign
0.58
PhyloP100
-0.49
PromoterAI
-0.015
Neutral

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

Other links and lift over

dbSNP: rs191169882; hg19: chr7-66093882; API