chr20-2103140-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_080836.4(STK35):āc.667C>Gā(p.Arg223Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000835 in 1,604,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_080836.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK35 | NM_080836.4 | c.667C>G | p.Arg223Gly | missense_variant | 2/4 | ENST00000381482.8 | |
STK35 | XM_011529174.4 | c.667C>G | p.Arg223Gly | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK35 | ENST00000381482.8 | c.667C>G | p.Arg223Gly | missense_variant | 2/4 | 5 | NM_080836.4 | P1 | |
STK35 | ENST00000493263.1 | c.250C>G | p.Arg84Gly | missense_variant, NMD_transcript_variant | 1/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000455 AC: 69AN: 151578Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000115 AC: 26AN: 226592Hom.: 0 AF XY: 0.000111 AC XY: 14AN XY: 125730
GnomAD4 exome AF: 0.0000447 AC: 65AN: 1452708Hom.: 0 Cov.: 32 AF XY: 0.0000374 AC XY: 27AN XY: 722798
GnomAD4 genome AF: 0.000455 AC: 69AN: 151698Hom.: 0 Cov.: 33 AF XY: 0.000499 AC XY: 37AN XY: 74170
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.667C>G (p.R223G) alteration is located in exon 2 (coding exon 2) of the STK35 gene. This alteration results from a C to G substitution at nucleotide position 667, causing the arginine (R) at amino acid position 223 to be replaced by a glycine (G). 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