rs528301360
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006282.5(STK4):c.526-7A>C 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 0.00000127 in 1,572,978 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_006282.5 splice_region, splice_polypyrimidine_tract, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK4 | NM_006282.5 | c.526-7A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000372806.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK4 | ENST00000372806.8 | c.526-7A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006282.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000695 AC: 1AN: 143850Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00000849 AC: 2AN: 235660Hom.: 0 AF XY: 0.0000157 AC XY: 2AN XY: 127768
GnomAD4 exome AF: 7.00e-7 AC: 1AN: 1429028Hom.: 0 Cov.: 31 AF XY: 0.00000141 AC XY: 1AN XY: 710484
GnomAD4 genome ? AF: 0.00000695 AC: 1AN: 143950Hom.: 0 Cov.: 29 AF XY: 0.0000144 AC XY: 1AN XY: 69520
ClinVar
Submissions by phenotype
Combined immunodeficiency due to STK4 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at