rs6833812

Variant names:

• chr4-5108413-G-A
• rs6833812
• NM_018401.3:c.53-31492G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-5108413-G-A
• chr4-5108413-G-C
• chr4-5108413-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018401.3(STK32B):​c.53-31492G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,064 control chromosomes in the GnomAD database, including 3,325 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 0.21 (3325 hom., cov: 32)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK32B	NM_018401.3	c.53-31492G>A		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.53-31492G>A		intron_variant	Intron 1 of 11	1	NM_018401.3	ENSP00000282908.5
STK32B	ENST00000512018.5	n.53-31492G>A		intron_variant	Intron 1 of 12	1		ENSP00000422820.1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31794 AN: 151948 Hom.: 3323 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.209 AC: 31801 AN: 152064 Hom.: 3325 Cov.: 32 AF XY: 0.208 AC XY: 15460 AN XY: 74328

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.221

Alfa AF: 0.204 Hom.: 3222

Bravo AF: 0.208

Asia WGS AF: 0.200 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.75

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: rs6833812; hg19: chr4-5110140;