20-2160408-G-A

Position:

• chr20-2160408-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000493263.1(STK35):​c.*38-12896G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,926 control chromosomes in the GnomAD database, including 15,414 homozygotes. 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 0.42 (15414 hom., cov: 31)
• Consequence: STK35 ENST00000493263.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK35	ENST00000493263.1	c.*38-12896G>A		intron_variant, NMD_transcript_variant		1		ENSP00000426612

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63383 AN: 151808 Hom.: 15367 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.405

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.418 AC: 63486 AN: 151926 Hom.: 15414 Cov.: 31 AF XY: 0.426 AC XY: 31619 AN XY: 74240

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.414

Alfa AF: 0.318 Hom.: 1695

Bravo AF: 0.441

Asia WGS AF: 0.769 AC: 2671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6047134; hg19: chr20-2141054;