5-147264552-C-T

Variant summary

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

The NM_001112724.2(STK32A):c.53-13572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,096 control chromosomes in the GnomAD database, including 47,134 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 0.78 (47134 hom., cov: 32)
• Consequence: STK32A NM_001112724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

Genes affected

STK32A (HGNC:28317): (serine/threonine kinase 32A) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in intracellular signal transduction and peptidyl-serine phosphorylation. Predicted to be located in plasma membrane. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK32A	NM_001112724.2	c.53-13572C>T		intron_variant		ENST00000397936.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK32A	ENST00000397936.8	c.53-13572C>T		intron_variant		5	NM_001112724.2	P1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119054 AN: 151978 Hom.: 47085 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.783 AC: 119154 AN: 152096 Hom.: 47134 Cov.: 32 AF XY: 0.779 AC XY: 57874 AN XY: 74340

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.805

Alfa AF: 0.753 Hom.: 21183

Bravo AF: 0.802

Asia WGS AF: 0.674 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.2
Dann	Benign	0.50

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: rs2895680; hg19: chr5-146644115;