4-5153395-T-C

Position:

• chr4-5153395-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.108+13435T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0648 in 152,106 control chromosomes in the GnomAD database, including 577 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 0.065 (577 hom., cov: 32)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK32B	NM_018401.3	c.108+13435T>C		intron_variant		ENST00000282908.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK32B	ENST00000282908.10	c.108+13435T>C		intron_variant		1	NM_018401.3	P1
STK32B	ENST00000510398.1	c.-34+13435T>C		intron_variant		1
STK32B	ENST00000512018.5	c.*62+13089T>C		intron_variant, NMD_transcript_variant		1
STK32B	ENST00000512636.5	c.-34+13435T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0647 AC: 9828 AN: 151994 Hom.: 572 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0318

Gnomad OTH AF: 0.0671

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

GnomAD4 genome AF: 0.0648 AC: 9864 AN: 152106 Hom.: 577 Cov.: 32 AF XY: 0.0654 AC XY: 4860 AN XY: 74346

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0356

Gnomad4 FIN AF: 0.0146

Gnomad4 NFE AF: 0.0318

Gnomad4 OTH AF: 0.0664

Alfa AF: 0.0610 Hom.: 177

Bravo AF: 0.0781

Asia WGS AF: 0.0290 AC: 101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.52

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: rs10516172; hg19: chr4-5155122;