20-2165639-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493263.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK35	ENST00000493263.1	TSL:1	n.*38-7665C>T		intron	N/A	ENSP00000426612.1	A0A0C4DGC9

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

African (AFR) AF: 0.197 AC: 8181 AN: 41490

American (AMR) AF: 0.217 AC: 3317 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3468

East Asian (EAS) AF: 0.0558 AC: 289 AN: 5176

South Asian (SAS) AF: 0.191 AC: 924 AN: 4826

European-Finnish (FIN) AF: 0.341 AC: 3595 AN: 10546

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23170 AN: 67972

Other (OTH) AF: 0.294 AC: 622 AN: 2114

Alfa AF: 0.288 Hom.: 4648

Bravo AF: 0.262

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.32
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs6047163; hg19: chr20-2146285;