4-5134403-C-T

Variant names:

• chr4-5134403-C-T
• rs6856163
• NM_018401.3:c.53-5502C>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.53-5502C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,126 control chromosomes in the GnomAD database, including 52,343 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 0.83 (52343 hom., cov: 32)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018401.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32B	NM_018401.3	MANE Select	c.53-5502C>T		intron	N/A	NP_060871.1
	STK32B	NM_001345969.2		c.53-5502C>T		intron	N/A	NP_001332898.1
	STK32B	NM_001306082.2		c.-199-5502C>T		intron	N/A	NP_001293011.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32B	ENST00000282908.10	TSL:1 MANE Select	c.53-5502C>T		intron	N/A	ENSP00000282908.5
	STK32B	ENST00000512018.5	TSL:1	n.53-5502C>T		intron	N/A	ENSP00000422820.1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125709 AN: 152008 Hom.: 52311 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.827 AC: 125795 AN: 152126 Hom.: 52343 Cov.: 32 AF XY: 0.829 AC XY: 61651 AN XY: 74392

African (AFR) AF: 0.712 AC: 29519 AN: 41436

American (AMR) AF: 0.844 AC: 12895 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3009 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4442 AN: 5184

South Asian (SAS) AF: 0.876 AC: 4224 AN: 4820

European-Finnish (FIN) AF: 0.859 AC: 9111 AN: 10602

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59904 AN: 68016

Other (OTH) AF: 0.842 AC: 1774 AN: 2106

Alfa AF: 0.857 Hom.: 78679

Bravo AF: 0.821

Asia WGS AF: 0.833 AC: 2899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.32
PhyloP100		-1.3
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: rs6856163; hg19: chr4-5136130;