chr18-26455775-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001142730.3(KCTD1):c.2566G>A(p.Val856Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000963 in 1,614,070 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001142730.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD1 | NM_001142730.3 | c.2566G>A | p.Val856Ile | missense_variant | 5/5 | ENST00000580059.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD1 | ENST00000580059.7 | c.2566G>A | p.Val856Ile | missense_variant | 5/5 | 3 | NM_001142730.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000828 AC: 126AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000541 AC: 136AN: 251350Hom.: 0 AF XY: 0.000530 AC XY: 72AN XY: 135858
GnomAD4 exome AF: 0.000977 AC: 1428AN: 1461826Hom.: 3 Cov.: 32 AF XY: 0.000927 AC XY: 674AN XY: 727224
GnomAD4 genome ? AF: 0.000828 AC: 126AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000779 AC XY: 58AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.2566G>A (p.V856I) 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 2566, causing the valine (V) at amino acid position 856 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at