chr20-2160408-G-A

Variant names:

• chr20-2160408-G-A
• rs6047134
• ENST00000493263.1:n.*38-12896G>A

Variant summary

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

The ENST00000493263.1(STK35):​n.*38-12896G>A variant causes a intron 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK35	ENST00000493263.1	n.*38-12896G>A		intron_variant	Intron 2 of 3	1		ENSP00000426612.1

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;