rs4017782

Variant names:

• chr4-5425964-G-A
• rs4017782
• NM_018401.3:c.562+9030G>A

Variant summary

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

The NM_018401.3(STK32B):​c.562+9030G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,160 control chromosomes in the GnomAD database, including 2,784 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 0.16 (2784 hom., cov: 33)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 1 publications found

Genes affected

STK32B (HGNC:14217): (serine/threonine kinase 32B) This gene encodes a serine-threonine protein kinase. Serine-threonine kinases transfer phosphate molecules to the oxygen atoms of serine and threonine. A genomic deletion affecting this gene has been associated with Ellis-van Creveld syndrome, an autosomal recessive skeletal dysplasia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK32B	NM_018401.3	c.562+9030G>A		intron_variant	Intron 6 of 11	ENST00000282908.10	NP_060871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK32B	ENST00000282908.10	c.562+9030G>A		intron_variant	Intron 6 of 11	1	NM_018401.3	ENSP00000282908.5

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24605 AN: 152040 Hom.: 2773 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.162 AC: 24650 AN: 152160 Hom.: 2784 Cov.: 33 AF XY: 0.165 AC XY: 12267 AN XY: 74374

African (AFR) AF: 0.288 AC: 11940 AN: 41482

American (AMR) AF: 0.153 AC: 2344 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2123 AN: 5168

South Asian (SAS) AF: 0.222 AC: 1073 AN: 4824

European-Finnish (FIN) AF: 0.103 AC: 1096 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0784 AC: 5336 AN: 68020

Other (OTH) AF: 0.156 AC: 329 AN: 2108

Alfa AF: 0.105 Hom.: 5678

Bravo AF: 0.170

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.67
DANN	Benign	0.77
PhyloP100		-2.8
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: rs4017782; hg19: chr4-5427691;