chr5-172061141-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005990.4(STK10):c.2210G>T(p.Arg737Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,610,248 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R737Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_005990.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK10 | NM_005990.4 | c.2210G>T | p.Arg737Leu | missense_variant, splice_region_variant | 14/19 | ENST00000176763.10 | |
STK10 | XM_047417627.1 | c.1820G>T | p.Arg607Leu | missense_variant, splice_region_variant | 11/16 | ||
STK10 | XM_047417628.1 | c.1661G>T | p.Arg554Leu | missense_variant, splice_region_variant | 13/18 | ||
STK10 | XM_047417629.1 | c.1526G>T | p.Arg509Leu | missense_variant, splice_region_variant | 12/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK10 | ENST00000176763.10 | c.2210G>T | p.Arg737Leu | missense_variant, splice_region_variant | 14/19 | 1 | NM_005990.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 151918Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000129 AC: 32AN: 248312Hom.: 0 AF XY: 0.0000595 AC XY: 8AN XY: 134350
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1458330Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 725584
GnomAD4 genome ? AF: 0.0000724 AC: 11AN: 151918Hom.: 0 Cov.: 31 AF XY: 0.0000809 AC XY: 6AN XY: 74174
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2023 | The c.2210G>T (p.R737L) alteration is located in exon 14 (coding exon 14) of the STK10 gene. This alteration results from a G to T substitution at nucleotide position 2210, causing the arginine (R) at amino acid position 737 to be replaced by a leucine (L). 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