chr5-172082337-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005990.4(STK10):c.1978A>G(p.Met660Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000284 in 1,410,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005990.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK10 | NM_005990.4 | c.1978A>G | p.Met660Val | missense_variant | 12/19 | ENST00000176763.10 | |
STK10 | XM_047417627.1 | c.1588A>G | p.Met530Val | missense_variant | 9/16 | ||
STK10 | XM_047417628.1 | c.1429A>G | p.Met477Val | missense_variant | 11/18 | ||
STK10 | XM_047417629.1 | c.1294A>G | p.Met432Val | missense_variant | 10/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK10 | ENST00000176763.10 | c.1978A>G | p.Met660Val | missense_variant | 12/19 | 1 | NM_005990.4 | P1 | |
STK10 | ENST00000522879.1 | n.69A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000478 AC: 1AN: 209036Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 113684
GnomAD4 exome AF: 0.00000284 AC: 4AN: 1410034Hom.: 0 Cov.: 30 AF XY: 0.00000286 AC XY: 2AN XY: 698854
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.1978A>G (p.M660V) alteration is located in exon 12 (coding exon 12) of the STK10 gene. This alteration results from a A to G substitution at nucleotide position 1978, causing the methionine (M) at amino acid position 660 to be replaced by a valine (V). 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