rs3007220

Positions:

• chr1-36376248-G-C

Variant summary

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

The NM_001282547.2(STK40):​c.-9+9475C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,156 control chromosomes in the GnomAD database, including 57,934 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 0.87 (57934 hom., cov: 31)
• Consequence: STK40 NM_001282547.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK40	NM_001282547.2	c.-9+9475C>G		intron_variant		ENST00000373132.4
STK40	NM_001282546.2	c.-9+9475C>G		intron_variant
STK40	NM_032017.3	c.-245-8164C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK40	ENST00000373132.4	c.-9+9475C>G		intron_variant		1	NM_001282547.2	A1

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132214 AN: 152038 Hom.: 57869 Cov.: 31

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.870 AC: 132338 AN: 152156 Hom.: 57934 Cov.: 31 AF XY: 0.870 AC XY: 64670 AN XY: 74346

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.856

Alfa AF: 0.845 Hom.: 6759

Bravo AF: 0.876

Asia WGS AF: 0.963 AC: 3351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.41

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: rs3007220; hg19: chr1-36841849;