chr20-2165639-C-T

Variant names:

• chr20-2165639-C-T
• rs6047163
• ENST00000493263.1:n.*38-7665C>T

Variant summary

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

The ENST00000493263.1(STK35):​n.*38-7665C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,070 control chromosomes in the GnomAD database, including 6,145 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 0.27 (6145 hom., cov: 32)
• Consequence: STK35 ENST00000493263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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.*38-7665C>T		intron_variant	Intron 2 of 3	1		ENSP00000426612.1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41537 AN: 151952 Hom.: 6143 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.273 AC: 41565 AN: 152070 Hom.: 6145 Cov.: 32 AF XY: 0.270 AC XY: 20045 AN XY: 74332

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.294

Alfa AF: 0.278 Hom.: 2984

Bravo AF: 0.262

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6047163; hg19: chr20-2146285;