chr16-2682589-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018992.4(KCTD5):c.41G>T(p.Gly14Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000236 in 1,269,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018992.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD5 | NM_018992.4 | c.41G>T | p.Gly14Val | missense_variant | 1/6 | ENST00000301738.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD5 | ENST00000301738.9 | c.41G>T | p.Gly14Val | missense_variant | 1/6 | 1 | NM_018992.4 | P1 | |
KCTD5 | ENST00000564195.1 | c.41G>T | p.Gly14Val | missense_variant | 1/5 | 5 | |||
KCTD5 | ENST00000564246.1 | n.57G>T | non_coding_transcript_exon_variant | 1/4 | 3 | ||||
KCTD5 | ENST00000570005.5 | n.62G>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.0000104 AC: 1AN: 96212Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 54946
GnomAD4 exome AF: 0.00000236 AC: 3AN: 1269924Hom.: 0 Cov.: 31 AF XY: 0.00000321 AC XY: 2AN XY: 623320
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2023 | The c.41G>T (p.G14V) alteration is located in exon 1 (coding exon 1) of the KCTD5 gene. This alteration results from a G to T substitution at nucleotide position 41, causing the glycine (G) at amino acid position 14 to be replaced by a valine (V). 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