11-78173834-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001029859.3(KCTD21):c.721T>G(p.Ser241Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000057 in 1,614,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. S241P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001029859.3 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 |
---|---|---|---|---|---|---|---|
KCTD21 | NM_001029859.3 | c.721T>G | p.Ser241Ala | missense_variant | 2/2 | ENST00000340067.4 | |
KCTD21-AS1 | NR_102280.1 | n.940A>C | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCTD21 | ENST00000340067.4 | c.721T>G | p.Ser241Ala | missense_variant | 2/2 | 1 | NM_001029859.3 | P1 | |
KCTD21-AS1 | ENST00000662186.1 | n.842A>C | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152188Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251286Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135810
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000605 AC XY: 44AN XY: 727242
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152306Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.721T>G (p.S241A) alteration is located in exon 2 (coding exon 1) of the KCTD21 gene. This alteration results from a T to G substitution at nucleotide position 721, causing the serine (S) at amino acid position 241 to be replaced by an alanine (A). 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