7-66629086-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_153033.5(KCTD7):c.22G>A(p.Glu8Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000392 in 1,532,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153033.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCTD7 | NM_153033.5 | c.22G>A | p.Glu8Lys | missense_variant | 1/4 | ENST00000639828.2 | NP_694578.1 | |
KCTD7 | NM_001167961.2 | c.22G>A | p.Glu8Lys | missense_variant | 1/5 | NP_001161433.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151920Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000130 AC: 2AN: 153898Hom.: 0 AF XY: 0.0000118 AC XY: 1AN XY: 84512
GnomAD4 exome AF: 0.00000290 AC: 4AN: 1380580Hom.: 0 Cov.: 34 AF XY: 0.00000293 AC XY: 2AN XY: 683148
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151920Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74214
ClinVar
Submissions by phenotype
Progressive myoclonic epilepsy type 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 15, 2018 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with KCTD7-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with lysine at codon 8 of the KCTD7 protein (p.Glu8Lys). The glutamic acid residue is moderately conserved and there is a small physicochemical difference between glutamic acid and lysine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at