rs11583322

Variant names:

• chr1-36356711-T-C
• rs11583322
• NM_001282547.2:c.343-1278A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001282547.2(STK40):​c.343-1278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,940 control chromosomes in the GnomAD database, including 7,859 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 0.30 (7859 hom., cov: 31)
• Consequence: STK40 NM_001282547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 8 publications found

Genes affected

STK40 (HGNC:21373): (serine/threonine kinase 40) Predicted to enable ATP binding activity; protein serine kinase activity; and protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation. Predicted to act upstream of or within several processes, including glycogen metabolic process; lung development; and respiratory system process. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK40	NM_001282547.2	c.343-1278A>G		intron_variant	Intron 4 of 10	ENST00000373132.4	NP_001269476.1
STK40	NM_001282546.2	c.358-1278A>G		intron_variant	Intron 4 of 10		NP_001269475.1
STK40	NM_032017.3	c.343-1278A>G		intron_variant	Intron 5 of 11		NP_114406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK40	ENST00000373132.4	c.343-1278A>G		intron_variant	Intron 4 of 10	1	NM_001282547.2	ENSP00000362224.4

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44925 AN: 151822 Hom.: 7859 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.296 AC: 44917 AN: 151940 Hom.: 7859 Cov.: 31 AF XY: 0.296 AC XY: 21996 AN XY: 74250

African (AFR) AF: 0.115 AC: 4753 AN: 41472

American (AMR) AF: 0.261 AC: 3992 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3468

East Asian (EAS) AF: 0.159 AC: 823 AN: 5170

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4820

European-Finnish (FIN) AF: 0.457 AC: 4796 AN: 10498

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26797 AN: 67930

Other (OTH) AF: 0.307 AC: 647 AN: 2108

Alfa AF: 0.361 Hom.: 12972

Bravo AF: 0.273

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.37
PhyloP100		-0.15
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: rs11583322; hg19: chr1-36822312;