chr15-31327545-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_015995.4(KLF13):āc.333A>Cā(p.Glu111Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E111A) has been classified 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.333A>C | p.Glu111Asp | missense_variant | 1/2 | ENST00000307145.4 | |
KLF13 | NM_001302461.2 | c.333A>C | p.Glu111Asp | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF13 | ENST00000307145.4 | c.333A>C | p.Glu111Asp | missense_variant | 1/2 | 1 | NM_015995.4 | P1 | |
KLF13 | ENST00000558921.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 3AN: 145724Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000210 AC: 2AN: 953028Hom.: 0 Cov.: 32 AF XY: 0.00000223 AC XY: 1AN XY: 448030
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000137 AC: 2AN: 145842Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 71082
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.333A>C (p.E111D) alteration is located in exon 1 (coding exon 1) of the KLF13 gene. This alteration results from a A to C substitution at nucleotide position 333, causing the glutamic acid (E) at amino acid position 111 to be replaced by an aspartic acid (D). 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