13-73813270-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_007249.5(KLF12):c.688G>A(p.Gly230Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLF12 | NM_001400136.1 | c.688G>A | p.Gly230Ser | missense_variant | Exon 5 of 8 | NP_001387065.1 | ||
KLF12 | NM_001400139.1 | c.688G>A | p.Gly230Ser | missense_variant | Exon 5 of 8 | NP_001387068.1 | ||
KLF12 | NM_001400141.1 | c.688G>A | p.Gly230Ser | missense_variant | Exon 5 of 8 | NP_001387070.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLF12 | ENST00000377669.7 | c.688G>A | p.Gly230Ser | missense_variant | Exon 5 of 8 | 1 | ENSP00000366897.2 | |||
KLF12 | ENST00000703967.1 | c.688G>A | p.Gly230Ser | missense_variant | Exon 5 of 8 | ENSP00000515592.1 | ||||
KLF12 | ENST00000472022.1 | n.722G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251118Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135706
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461720Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727168
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.688G>A (p.G230S) alteration is located in exon 5 (coding exon 4) of the KLF12 gene. This alteration results from a G to A substitution at nucleotide position 688, causing the glycine (G) at amino acid position 230 to be replaced by a serine (S). 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