5-144207171-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020768.4(KCTD16):c.457C>A(p.Pro153Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000725 in 1,612,734 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P153L) has been classified as Uncertain significance.
Frequency
Consequence
NM_020768.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD16 | NM_020768.4 | c.457C>A | p.Pro153Thr | missense_variant | 3/4 | ENST00000512467.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD16 | ENST00000512467.6 | c.457C>A | p.Pro153Thr | missense_variant | 3/4 | 1 | NM_020768.4 | P1 | |
KCTD16 | ENST00000507359.3 | c.457C>A | p.Pro153Thr | missense_variant | 2/3 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250276Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135212
GnomAD4 exome AF: 0.0000712 AC: 104AN: 1460616Hom.: 0 Cov.: 31 AF XY: 0.0000729 AC XY: 53AN XY: 726530
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2024 | The c.457C>A (p.P153T) alteration is located in exon 3 (coding exon 1) of the KCTD16 gene. This alteration results from a C to A substitution at nucleotide position 457, causing the proline (P) at amino acid position 153 to be replaced by a threonine (T). 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