4-5219851-C-T

Position:

• chr4-5219851-C-T

Variant summary

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

The NM_018401.3(STK32B):​c.260+51401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,242 control chromosomes in the GnomAD database, including 55,673 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 0.85 (55673 hom., cov: 32)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK32B	NM_018401.3	c.260+51401C>T		intron_variant		ENST00000282908.10	NP_060871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK32B	ENST00000282908.10	c.260+51401C>T		intron_variant		1	NM_018401.3	ENSP00000282908	P1

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129855 AN: 152124 Hom.: 55640 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.853 AC: 129937 AN: 152242 Hom.: 55673 Cov.: 32 AF XY: 0.852 AC XY: 63428 AN XY: 74410

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.857

Alfa AF: 0.846 Hom.: 72953

Bravo AF: 0.847

Asia WGS AF: 0.924 AC: 3212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.9
DANN	Benign	0.77

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: rs1812310; hg19: chr4-5221578;