rs78647349

chr4-5235426-G-Achr4-5235426-G-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+66976G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0364 in 152,192 control chromosomes in the GnomAD database, including 136 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 0.036 (136 hom., cov: 33)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK32B	NM_018401.3	c.260+66976G>A		intron_variant		ENST00000282908.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK32B	ENST00000282908.10	c.260+66976G>A		intron_variant		1	NM_018401.3	P1

Frequencies

GnomAD3 genomes AF: 0.0364 AC: 5541 AN: 152074 Hom.: 136 Cov.: 33

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0193

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.00904

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0364 AC: 5537 AN: 152192 Hom.: 136 Cov.: 33 AF XY: 0.0360 AC XY: 2677 AN XY: 74422

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.0193

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.0540

Gnomad4 SAS AF: 0.0833

Gnomad4 FIN AF: 0.00904

Gnomad4 NFE AF: 0.0304

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0140 Hom.: 7

Bravo AF: 0.0366

Asia WGS AF: 0.0580 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.14
Dann	Benign	0.45

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: rs78647349; hg19: chr4-5237153;