16-2682561-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018992.4(KCTD5):c.13C>T(p.His5Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000426 in 1,408,948 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD5 | NM_018992.4 | c.13C>T | p.His5Tyr | missense_variant | 1/6 | ENST00000301738.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD5 | ENST00000301738.9 | c.13C>T | p.His5Tyr | missense_variant | 1/6 | 1 | NM_018992.4 | P1 | |
KCTD5 | ENST00000564195.1 | c.13C>T | p.His5Tyr | missense_variant | 1/5 | 5 | |||
KCTD5 | ENST00000564246.1 | n.29C>T | non_coding_transcript_exon_variant | 1/4 | 3 | ||||
KCTD5 | ENST00000570005.5 | n.34C>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000398 AC: 5AN: 1256744Hom.: 0 Cov.: 31 AF XY: 0.00000488 AC XY: 3AN XY: 614570
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.13C>T (p.H5Y) alteration is located in exon 1 (coding exon 1) of the KCTD5 gene. This alteration results from a C to T substitution at nucleotide position 13, causing the histidine (H) at amino acid position 5 to be replaced by a tyrosine (Y). 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