4-5219811-G-C

Position:

• chr4-5219811-G-C

Variant summary

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

The NM_018401.3(STK32B):​c.260+51361G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,128 control chromosomes in the GnomAD database, including 34,206 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 0.66 (34206 hom., cov: 33)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK32B	NM_018401.3	c.260+51361G>C		intron_variant		ENST00000282908.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK32B	ENST00000282908.10	c.260+51361G>C		intron_variant		1	NM_018401.3	P1

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100983 AN: 152010 Hom.: 34179 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.664 AC: 101045 AN: 152128 Hom.: 34206 Cov.: 33 AF XY: 0.665 AC XY: 49464 AN XY: 74364

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.663

Alfa AF: 0.621 Hom.: 1940

Bravo AF: 0.660

Asia WGS AF: 0.712 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.40

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: rs2008242; hg19: chr4-5221538;