20-2122618-G-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_080836.4(STK35):c.*37+5203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000395 in 151,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Consequence
STK35
NM_080836.4 intron
NM_080836.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0710
Genes affected
STK35 (HGNC:16254): (serine/threonine kinase 35) The protein encoded by this gene is a kinase that is predominantly found in the nucleus. However, it can interact with PDLIM1/CLP-36 in the cytoplasm and localize to actin stress fibers. The encoded protein may be a regulator of actin stress fibers in nonmuscle cells. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS2
High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK35 | NM_080836.4 | c.*37+5203G>A | intron_variant | ENST00000381482.8 | NP_543026.2 | |||
LOC124900458 | XR_007067499.1 | n.4932G>A | non_coding_transcript_exon_variant | 1/2 | ||||
STK35 | XM_011529174.4 | c.892+19253G>A | intron_variant | XP_011527476.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STK35 | ENST00000381482.8 | c.*37+5203G>A | intron_variant | 5 | NM_080836.4 | ENSP00000370891 | P1 | |||
STK35 | ENST00000493263.1 | c.*37+5203G>A | intron_variant, NMD_transcript_variant | 1 | ENSP00000426612 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151966Hom.: 0 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74194
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at