15-31327616-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_015995.4(KLF13):c.404G>A(p.Arg135Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000166 in 1,329,212 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_015995.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF13 | NM_015995.4 | c.404G>A | p.Arg135Gln | missense_variant | 1/2 | ENST00000307145.4 | |
KLF13 | NM_001302461.2 | c.404G>A | p.Arg135Gln | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF13 | ENST00000307145.4 | c.404G>A | p.Arg135Gln | missense_variant | 1/2 | 1 | NM_015995.4 | P1 | |
KLF13 | ENST00000558921.1 | n.50G>A | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000134 AC: 2AN: 148964Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000169 AC: 20AN: 1180248Hom.: 0 Cov.: 33 AF XY: 0.0000156 AC XY: 9AN XY: 575600
GnomAD4 genome ? AF: 0.0000134 AC: 2AN: 148964Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72634
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2023 | The c.404G>A (p.R135Q) alteration is located in exon 1 (coding exon 1) of the KLF13 gene. This alteration results from a G to A substitution at nucleotide position 404, causing the arginine (R) at amino acid position 135 to be replaced by a glutamine (Q). 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