rs3809831
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001363642.1(KCTD11):c.*709C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 167,144 control chromosomes in the GnomAD database, including 934 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.095 ( 865 hom., cov: 32)
Exomes 𝑓: 0.099 ( 69 hom. )
Consequence
KCTD11
NM_001363642.1 3_prime_UTR
NM_001363642.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.232
Genes affected
KCTD11 (HGNC:21302): (potassium channel tetramerization domain containing 11) Enables identical protein binding activity. Predicted to be involved in positive regulation of neuron differentiation. Predicted to act upstream of or within negative regulation of neuroblast proliferation and negative regulation of smoothened signaling pathway. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCTD11 | NM_001363642.1 | c.*709C>A | 3_prime_UTR_variant | 1/1 | ENST00000333751.8 | ||
KCTD11 | NM_001002914.3 | c.*709C>A | 3_prime_UTR_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD11 | ENST00000333751.8 | c.*709C>A | 3_prime_UTR_variant | 1/1 | NM_001363642.1 | ||||
ENST00000572417.1 | n.275+320G>T | intron_variant, non_coding_transcript_variant | 2 | ||||||
KCTD11 | ENST00000576980.2 | c.*709C>A | 3_prime_UTR_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0945 AC: 14358AN: 151980Hom.: 859 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
14358
AN:
151980
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0989 AC: 1488AN: 15046Hom.: 69 Cov.: 0 AF XY: 0.104 AC XY: 746AN XY: 7182
GnomAD4 exome
AF:
AC:
1488
AN:
15046
Hom.:
Cov.:
0
AF XY:
AC XY:
746
AN XY:
7182
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0946 AC: 14386AN: 152098Hom.: 865 Cov.: 32 AF XY: 0.0951 AC XY: 7070AN XY: 74364
GnomAD4 genome
?
AF:
AC:
14386
AN:
152098
Hom.:
Cov.:
32
AF XY:
AC XY:
7070
AN XY:
74364
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
467
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at