4-5083198-T-C

Position:

• chr4-5083198-T-C

Variant summary

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

The NM_018401.3(STK32B):​c.52+31283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,186 control chromosomes in the GnomAD database, including 1,034 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 0.10 (1034 hom., cov: 33)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.906

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK32B	NM_018401.3	c.52+31283T>C		intron_variant		ENST00000282908.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK32B	ENST00000282908.10	c.52+31283T>C		intron_variant		1	NM_018401.3	P1
STK32B	ENST00000512018.5	c.52+31283T>C		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15956 AN: 152068 Hom.: 1034 Cov.: 33

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.105 AC: 15955 AN: 152186 Hom.: 1034 Cov.: 33 AF XY: 0.106 AC XY: 7868 AN XY: 74404

Gnomad4 AFR AF: 0.0342

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0970

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.112

Alfa AF: 0.124 Hom.: 236

Bravo AF: 0.108

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.46

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: rs1447285; hg19: chr4-5084925;