chr22-37051816-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001282684.2(KCTD17):c.56C>T(p.Ala19Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. A19T) has been classified as Benign.
Frequency
Consequence
NM_001282684.2 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 |
---|---|---|---|---|---|---|---|
KCTD17 | NM_001282684.2 | c.56C>T | p.Ala19Val | missense_variant | 1/9 | ENST00000403888.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD17 | ENST00000403888.8 | c.56C>T | p.Ala19Val | missense_variant | 1/9 | 1 | NM_001282684.2 | A2 | |
KCTD17 | ENST00000402077.8 | c.56C>T | p.Ala19Val | missense_variant | 1/8 | 1 | A2 | ||
KCTD17 | ENST00000610767.5 | c.56C>T | p.Ala19Val | missense_variant | 1/6 | 3 | P2 | ||
KCTD17 | ENST00000421900.5 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1136608Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 548362
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 17, 2023 | The c.77C>T (p.A26V) alteration is located in exon 1 (coding exon 1) of the KCTD17 gene. This alteration results from a C to T substitution at nucleotide position 77, causing the alanine (A) at amino acid position 26 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