chr18-26455895-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001142730.3(KCTD1):c.2446G>A(p.Glu816Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000378 in 1,612,810 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001142730.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCTD1 | NM_001142730.3 | c.2446G>A | p.Glu816Lys | missense_variant | Exon 5 of 5 | ENST00000580059.7 | NP_001136202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCTD1 | ENST00000580059.7 | c.2446G>A | p.Glu816Lys | missense_variant | Exon 5 of 5 | 3 | NM_001142730.3 | ENSP00000463041.2 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250742Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135558
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1460676Hom.: 0 Cov.: 32 AF XY: 0.0000330 AC XY: 24AN XY: 726416
GnomAD4 genome AF: 0.000131 AC: 20AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2446G>A (p.E816K) alteration is located in exon 5 (coding exon 5) of the KCTD1 gene. This alteration results from a G to A substitution at nucleotide position 2446, causing the glutamic acid (E) at amino acid position 816 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at