4-5158539-T-G

Variant names:

• chr4-5158539-T-G
• rs3890337
• NM_018401.3:c.109-9760T>G

Variant summary

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

The NM_018401.3(STK32B):​c.109-9760T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,098 control chromosomes in the GnomAD database, including 4,827 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 0.22 (4827 hom., cov: 32)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018401.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32B	NM_018401.3	MANE Select	c.109-9760T>G		intron	N/A	NP_060871.1
	STK32B	NM_001345969.2		c.109-9760T>G		intron	N/A	NP_001332898.1
	STK32B	NM_001306082.2		c.-33-9760T>G		intron	N/A	NP_001293011.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32B	ENST00000282908.10	TSL:1 MANE Select	c.109-9760T>G		intron	N/A	ENSP00000282908.5
	STK32B	ENST00000510398.1	TSL:1	c.-33-9760T>G		intron	N/A	ENSP00000420984.1
	STK32B	ENST00000512018.5	TSL:1	n.*63-9760T>G		intron	N/A	ENSP00000422820.1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34153 AN: 151980 Hom.: 4820 Cov.: 32

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.225 AC: 34175 AN: 152098 Hom.: 4827 Cov.: 32 AF XY: 0.224 AC XY: 16647 AN XY: 74370

African (AFR) AF: 0.0647 AC: 2684 AN: 41502

American (AMR) AF: 0.182 AC: 2779 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1095 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1613 AN: 5164

South Asian (SAS) AF: 0.259 AC: 1246 AN: 4814

European-Finnish (FIN) AF: 0.297 AC: 3141 AN: 10574

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20939 AN: 67978

Other (OTH) AF: 0.229 AC: 484 AN: 2112

Alfa AF: 0.287 Hom.: 2082

Bravo AF: 0.206

Asia WGS AF: 0.261 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.59
PhyloP100		-1.0
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: rs3890337; hg19: chr4-5160266;