4-5152946-G-A

Variant names:

• chr4-5152946-G-A
• rs7672067
• NM_018401.3:c.108+12986G>A

Variant summary

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

The NM_018401.3(STK32B):​c.108+12986G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,224 control chromosomes in the GnomAD database, including 51,000 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 0.82 (51000 hom., cov: 33)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.904 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.108+12986G>A		intron	N/A	NP_060871.1
	STK32B	NM_001345969.2		c.108+12986G>A		intron	N/A	NP_001332898.1
	STK32B	NM_001306082.2		c.-34+12640G>A		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.108+12986G>A		intron	N/A	ENSP00000282908.5
	STK32B	ENST00000510398.1	TSL:1	c.-34+12986G>A		intron	N/A	ENSP00000420984.1
	STK32B	ENST00000512018.5	TSL:1	n.*62+12640G>A		intron	N/A	ENSP00000422820.1

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124262 AN: 152106 Hom.: 50943 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.817 AC: 124377 AN: 152224 Hom.: 51000 Cov.: 33 AF XY: 0.819 AC XY: 60979 AN XY: 74430

African (AFR) AF: 0.878 AC: 36471 AN: 41542

American (AMR) AF: 0.792 AC: 12115 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2550 AN: 3472

East Asian (EAS) AF: 0.926 AC: 4792 AN: 5176

South Asian (SAS) AF: 0.800 AC: 3854 AN: 4818

European-Finnish (FIN) AF: 0.845 AC: 8955 AN: 10600

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53025 AN: 67992

Other (OTH) AF: 0.803 AC: 1698 AN: 2114

Alfa AF: 0.790 Hom.: 209063

Bravo AF: 0.815

Asia WGS AF: 0.864 AC: 3002 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	0.069
DANN	Benign	0.40
PhyloP100		-2.6
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: rs7672067; hg19: chr4-5154673;