chr15-31327584-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_015995.4(KLF13):c.372G>C(p.Glu124Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00442 in 1,219,838 control chromosomes in the GnomAD database, including 17 homozygotes. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_015995.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF13 | NM_015995.4 | c.372G>C | p.Glu124Asp | missense_variant | 1/2 | ENST00000307145.4 | |
KLF13 | NM_001302461.2 | c.372G>C | p.Glu124Asp | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF13 | ENST00000307145.4 | c.372G>C | p.Glu124Asp | missense_variant | 1/2 | 1 | NM_015995.4 | P1 | |
KLF13 | ENST00000558921.1 | n.18G>C | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00246 AC: 365AN: 148602Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00174 AC: 14AN: 8032Hom.: 0 AF XY: 0.00173 AC XY: 7AN XY: 4054
GnomAD4 exome AF: 0.00469 AC: 5026AN: 1071130Hom.: 17 Cov.: 33 AF XY: 0.00451 AC XY: 2313AN XY: 513142
GnomAD4 genome ? AF: 0.00245 AC: 365AN: 148708Hom.: 0 Cov.: 32 AF XY: 0.00215 AC XY: 156AN XY: 72582
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.372G>C (p.E124D) alteration is located in exon 1 (coding exon 1) of the KLF13 gene. This alteration results from a G to C substitution at nucleotide position 372, causing the glutamic acid (E) at amino acid position 124 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at