chr7-66631041-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153033.5(KCTD7):​c.144+1833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,032 control chromosomes in the GnomAD database, including 20,429 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 0.51 ( 20429 hom., cov: 33)

Consequence

KCTD7
NM_153033.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.135
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCTD7NM_153033.5 linkuse as main transcriptc.144+1833G>A intron_variant ENST00000639828.2 NP_694578.1
KCTD7NM_001167961.2 linkuse as main transcriptc.144+1833G>A intron_variant NP_001161433.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCTD7ENST00000639828.2 linkuse as main transcriptc.144+1833G>A intron_variant 2 NM_153033.5 ENSP00000492240 A1Q96MP8-1

Frequencies

GnomAD3 genomes
AF:
0.506
AC:
76870
AN:
151916
Hom.:
20400
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.660
Gnomad AMI
AF:
0.370
Gnomad AMR
AF:
0.485
Gnomad ASJ
AF:
0.378
Gnomad EAS
AF:
0.258
Gnomad SAS
AF:
0.361
Gnomad FIN
AF:
0.400
Gnomad MID
AF:
0.339
Gnomad NFE
AF:
0.473
Gnomad OTH
AF:
0.482
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.506
AC:
76945
AN:
152032
Hom.:
20429
Cov.:
33
AF XY:
0.500
AC XY:
37141
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.660
Gnomad4 AMR
AF:
0.484
Gnomad4 ASJ
AF:
0.378
Gnomad4 EAS
AF:
0.258
Gnomad4 SAS
AF:
0.361
Gnomad4 FIN
AF:
0.400
Gnomad4 NFE
AF:
0.473
Gnomad4 OTH
AF:
0.479
Alfa
AF:
0.467
Hom.:
15347
Bravo
AF:
0.518
Asia WGS
AF:
0.320
AC:
1112
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.87
DANN
Benign
0.65

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10263935; hg19: chr7-66096028; API