NM_013233.3:c.1327G>T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_013233.3(STK39):c.1327G>T(p.Asp443Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,612,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013233.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK39 | NM_013233.3 | c.1327G>T | p.Asp443Tyr | missense_variant | Exon 14 of 18 | ENST00000355999.5 | NP_037365.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STK39 | ENST00000355999.5 | c.1327G>T | p.Asp443Tyr | missense_variant | Exon 14 of 18 | 1 | NM_013233.3 | ENSP00000348278.4 | ||
STK39 | ENST00000487143.5 | n.427G>T | non_coding_transcript_exon_variant | Exon 5 of 9 | 1 | |||||
STK39 | ENST00000697205.1 | c.1264G>T | p.Asp422Tyr | missense_variant | Exon 13 of 17 | ENSP00000513185.1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000197 AC: 49AN: 249034Hom.: 0 AF XY: 0.000244 AC XY: 33AN XY: 135118
GnomAD4 exome AF: 0.000140 AC: 205AN: 1460688Hom.: 0 Cov.: 30 AF XY: 0.000158 AC XY: 115AN XY: 726618
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1327G>T (p.D443Y) alteration is located in exon 14 (coding exon 14) of the STK39 gene. This alteration results from a G to T substitution at nucleotide position 1327, causing the aspartic acid (D) at amino acid position 443 to be replaced by a tyrosine (Y). 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