13-73845935-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_007249.5(KLF12):c.562G>A(p.Val188Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,614,006 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007249.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLF12 | NM_001400136.1 | c.562G>A | p.Val188Met | missense_variant | Exon 4 of 8 | NP_001387065.1 | ||
KLF12 | NM_001400139.1 | c.562G>A | p.Val188Met | missense_variant | Exon 4 of 8 | NP_001387068.1 | ||
KLF12 | NM_001400141.1 | c.562G>A | p.Val188Met | missense_variant | Exon 4 of 8 | NP_001387070.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLF12 | ENST00000377669.7 | c.562G>A | p.Val188Met | missense_variant | Exon 4 of 8 | 1 | ENSP00000366897.2 | |||
KLF12 | ENST00000703967.1 | c.562G>A | p.Val188Met | missense_variant | Exon 4 of 8 | ENSP00000515592.1 | ||||
KLF12 | ENST00000472022.1 | n.596G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251344Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135830
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461824Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727210
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.562G>A (p.V188M) alteration is located in exon 4 (coding exon 3) of the KLF12 gene. This alteration results from a G to A substitution at nucleotide position 562, causing the valine (V) at amino acid position 188 to be replaced by a methionine (M). 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