rs1812310

Variant names:

• chr4-5219851-C-T
• rs1812310
• NM_018401.3:c.260+51401C>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.260+51401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,242 control chromosomes in the GnomAD database, including 55,673 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 0.85 (55673 hom., cov: 32)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32B	NM_018401.3	MANE Select	c.260+51401C>T		intron	N/A	NP_060871.1	Q9NY57-1
	STK32B	NM_001345969.2		c.260+51401C>T		intron	N/A	NP_001332898.1
	STK32B	NM_001306082.2		c.119+51401C>T		intron	N/A	NP_001293011.1	Q9NY57-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32B	ENST00000282908.10	TSL:1 MANE Select	c.260+51401C>T		intron	N/A	ENSP00000282908.5	Q9NY57-1
	STK32B	ENST00000510398.1	TSL:1	c.119+51401C>T		intron	N/A	ENSP00000420984.1	Q9NY57-2
	STK32B	ENST00000512018.5	TSL:1	n.*214+51401C>T		intron	N/A	ENSP00000422820.1	D6R9Y2

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129855 AN: 152124 Hom.: 55640 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.853 AC: 129937 AN: 152242 Hom.: 55673 Cov.: 32 AF XY: 0.852 AC XY: 63428 AN XY: 74410

African (AFR) AF: 0.887 AC: 36848 AN: 41562

American (AMR) AF: 0.744 AC: 11385 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2752 AN: 3472

East Asian (EAS) AF: 0.981 AC: 5091 AN: 5190

South Asian (SAS) AF: 0.859 AC: 4138 AN: 4816

European-Finnish (FIN) AF: 0.861 AC: 9104 AN: 10578

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57793 AN: 68010

Other (OTH) AF: 0.857 AC: 1812 AN: 2114

Alfa AF: 0.846 Hom.: 96194

Bravo AF: 0.847

Asia WGS AF: 0.924 AC: 3212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.9
DANN	Benign	0.77
PhyloP100		-0.65
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: rs1812310; hg19: chr4-5221578;