NM_080836.4:c.*37+5203G>T

Variant names:

• chr20-2122618-G-T
• rs6075668
• NM_080836.4:c.*37+5203G>T

Variant summary

Our verdict is Benign. The variant received -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
• 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]

LOC124900458 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STK35	NM_080836.4	c.*37+5203G>T		intron_variant	Intron 3 of 3	ENST00000381482.8	NP_543026.2
LOC124900458	XR_007067499.1	n.4932G>T		non_coding_transcript_exon_variant	Exon 1 of 2
STK35	XM_011529174.4	c.892+19253G>T		intron_variant	Intron 2 of 2		XP_011527476.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK35	ENST00000381482.8	c.*37+5203G>T		intron_variant	Intron 3 of 3	5	NM_080836.4	ENSP00000370891.3
STK35	ENST00000493263.1	n.*37+5203G>T		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.461 AC: 19083 AN: 41436

American (AMR) AF: 0.650 AC: 9940 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3466

East Asian (EAS) AF: 0.941 AC: 4860 AN: 5166

South Asian (SAS) AF: 0.650 AC: 3132 AN: 4816

European-Finnish (FIN) AF: 0.465 AC: 4902 AN: 10548

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32138 AN: 67974

Other (OTH) AF: 0.519 AC: 1094 AN: 2106

Alfa AF: 0.461 Hom.: 7982

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
PhyloP100		0.071
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6075668; hg19: chr20-2103264;