chr2-168075109-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_013233.3(STK39):c.1212G>A(p.Lys404=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.000343 in 1,614,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_013233.3 splice_region, synonymous
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 |
---|---|---|---|---|---|---|---|
STK39 | NM_013233.3 | c.1212G>A | p.Lys404= | splice_region_variant, synonymous_variant | 11/18 | ENST00000355999.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK39 | ENST00000355999.5 | c.1212G>A | p.Lys404= | splice_region_variant, synonymous_variant | 11/18 | 1 | NM_013233.3 | P1 | |
STK39 | ENST00000487143.5 | n.312G>A | splice_region_variant, non_coding_transcript_exon_variant | 2/9 | 1 | ||||
STK39 | ENST00000697205.1 | c.1212G>A | p.Lys404= | splice_region_variant, synonymous_variant | 11/17 |
Frequencies
GnomAD3 genomes AF: 0.00138 AC: 210AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000345 AC: 86AN: 249488Hom.: 0 AF XY: 0.000303 AC XY: 41AN XY: 135368
GnomAD4 exome AF: 0.000235 AC: 343AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.000208 AC XY: 151AN XY: 727242
GnomAD4 genome AF: 0.00138 AC: 210AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.00121 AC XY: 90AN XY: 74458
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at