chr8-98526806-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006281.4(STK3):c.1253T>G(p.Phe418Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000651 in 1,592,304 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006281.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK3 | NM_006281.4 | c.1253T>G | p.Phe418Cys | missense_variant | 10/11 | ENST00000419617.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK3 | ENST00000419617.7 | c.1253T>G | p.Phe418Cys | missense_variant | 10/11 | 1 | NM_006281.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000394 AC: 60AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000345 AC: 84AN: 243496Hom.: 0 AF XY: 0.000378 AC XY: 50AN XY: 132198
GnomAD4 exome AF: 0.000678 AC: 977AN: 1440190Hom.: 0 Cov.: 30 AF XY: 0.000658 AC XY: 471AN XY: 716202
GnomAD4 genome ? AF: 0.000394 AC: 60AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.1253T>G (p.F418C) alteration is located in exon 10 (coding exon 10) of the STK3 gene. This alteration results from a T to G substitution at nucleotide position 1253, causing the phenylalanine (F) at amino acid position 418 to be replaced by a cysteine (C). 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