chr17-7353348-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001363642.1(KCTD11):c.523G>T(p.Ala175Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000533 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 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. A175V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001363642.1 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 |
---|---|---|---|---|---|---|---|
KCTD11 | NM_001363642.1 | c.523G>T | p.Ala175Ser | missense_variant | 1/1 | ENST00000333751.8 | |
KCTD11 | NM_001002914.3 | c.406G>T | p.Ala136Ser | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD11 | ENST00000333751.8 | c.523G>T | p.Ala175Ser | missense_variant | 1/1 | NM_001363642.1 | |||
ENST00000572417.1 | n.276-516C>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
KCTD11 | ENST00000576980.2 | c.406G>T | p.Ala136Ser | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251390Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135906
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461794Hom.: 0 Cov.: 31 AF XY: 0.0000591 AC XY: 43AN XY: 727206
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2022 | The c.406G>T (p.A136S) alteration is located in exon 1 (coding exon 1) of the KCTD11 gene. This alteration results from a G to T substitution at nucleotide position 406, causing the alanine (A) at amino acid position 136 to be replaced by a serine (S). 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