4-5054047-C-T

Variant names:

• chr4-5054047-C-T
• rs9799796
• NM_018401.3:c.52+2132C>T

Variant summary

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

The NM_018401.3(STK32B):​c.52+2132C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,686 control chromosomes in the GnomAD database, including 6,767 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 0.29 (6767 hom., cov: 31)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK32B	NM_018401.3	c.52+2132C>T		intron_variant	Intron 1 of 11	ENST00000282908.10	NP_060871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK32B	ENST00000282908.10	c.52+2132C>T		intron_variant	Intron 1 of 11	1	NM_018401.3	ENSP00000282908.5
STK32B	ENST00000512018.5	n.52+2132C>T		intron_variant	Intron 1 of 12	1		ENSP00000422820.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43686 AN: 151570 Hom.: 6748 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.288 AC: 43736 AN: 151686 Hom.: 6767 Cov.: 31 AF XY: 0.290 AC XY: 21484 AN XY: 74124

African (AFR) AF: 0.386 AC: 15956 AN: 41350

American (AMR) AF: 0.267 AC: 4064 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3468

East Asian (EAS) AF: 0.481 AC: 2480 AN: 5160

South Asian (SAS) AF: 0.295 AC: 1415 AN: 4804

European-Finnish (FIN) AF: 0.269 AC: 2817 AN: 10466

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15347 AN: 67898

Other (OTH) AF: 0.267 AC: 560 AN: 2098

Alfa AF: 0.245 Hom.: 20189

Bravo AF: 0.297

Asia WGS AF: 0.400 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.47
PhyloP100		-0.18
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: rs9799796; hg19: chr4-5055774;