rs267607202
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_006563.5(KLF1):c.862A>T(p.Lys288Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000138 in 1,452,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Affects (no stars). Synonymous variant affecting the same amino acid position (i.e. K288K) has been classified as Uncertain significance.
Frequency
Consequence
NM_006563.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF1 | NM_006563.5 | c.862A>T | p.Lys288Ter | stop_gained | 2/3 | ENST00000264834.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF1 | ENST00000264834.6 | c.862A>T | p.Lys288Ter | stop_gained | 2/3 | 1 | NM_006563.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1452782Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 722068
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Fetal hemoglobin quantitative trait locus 6 Other:1
Affects, no assertion criteria provided | literature only | OMIM | Sep 01, 2010 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at