chr9-107487199-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004235.6(KLF4):c.1100-7C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000517 in 1,613,794 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004235.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF4 | NM_004235.6 | c.1100-7C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000374672.5 | |||
KLF4 | NM_001314052.2 | c.1195C>A | p.Pro399Thr | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF4 | ENST00000374672.5 | c.1100-7C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004235.6 | P1 | |||
KLF4 | ENST00000493306.1 | n.1460C>A | non_coding_transcript_exon_variant | 3/4 | 1 | ||||
KLF4 | ENST00000610832.1 | c.100-9C>A | splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
KLF4 | ENST00000497048.5 | n.1154-7C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00100 AC: 252AN: 250756Hom.: 3 AF XY: 0.000746 AC XY: 101AN XY: 135478
GnomAD4 exome AF: 0.000521 AC: 762AN: 1461470Hom.: 8 Cov.: 31 AF XY: 0.000465 AC XY: 338AN XY: 727020
GnomAD4 genome AF: 0.000479 AC: 73AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74472
ClinVar
Submissions by phenotype
KLF4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 20, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at