20-2122618-G-T

Position:

• chr20-2122618-G-T

Variant summary

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

The NM_080836.4(STK35):​c.*37+5203G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,000 control chromosomes in the GnomAD database, including 20,572 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 0.51 (20572 hom., cov: 32)
• Consequence: STK35 NM_080836.4 intron
• 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]

LOC124900458 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK35	NM_080836.4	c.*37+5203G>T		intron_variant		ENST00000381482.8	NP_543026.2
STK35	XM_011529174.4	c.892+19253G>T		intron_variant			XP_011527476.2
LOC124900458	XR_007067499.1	n.4932G>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK35	ENST00000381482.8	c.*37+5203G>T		intron_variant		5	NM_080836.4	ENSP00000370891.3
STK35	ENST00000493263.1	n.*37+5203G>T		intron_variant		1		ENSP00000426612.1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77273 AN: 151882 Hom.: 20543 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.509 AC: 77336 AN: 152000 Hom.: 20572 Cov.: 32 AF XY: 0.516 AC XY: 38330 AN XY: 74288

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.519

Alfa AF: 0.460 Hom.: 7070

Bravo AF: 0.518

Asia WGS AF: 0.796 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6075668; hg19: chr20-2103264;