rs4530574

Variant names:

• chr4-5147660-G-C
• rs4530574
• NM_018401.3:c.108+7700G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-5147660-G-C
• chr4-5147660-G-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.108+7700G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,712 control chromosomes in the GnomAD database, including 14,183 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 0.41 (14183 hom., cov: 32)
• Consequence: STK32B NM_018401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• 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 (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK32B	NM_018401.3	c.108+7700G>C		intron_variant	Intron 2 of 11	ENST00000282908.10	NP_060871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK32B	ENST00000282908.10	c.108+7700G>C		intron_variant	Intron 2 of 11	1	NM_018401.3	ENSP00000282908.5
STK32B	ENST00000510398.1	c.-34+7700G>C		intron_variant	Intron 2 of 11	1		ENSP00000420984.1
STK32B	ENST00000512018.5	n.*62+7354G>C		intron_variant	Intron 3 of 12	1		ENSP00000422820.1
STK32B	ENST00000512636.5	c.-34+7700G>C		intron_variant	Intron 2 of 10	5		ENSP00000423209.1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62759 AN: 151594 Hom.: 14170 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.414 AC: 62808 AN: 151712 Hom.: 14183 Cov.: 32 AF XY: 0.418 AC XY: 30998 AN XY: 74104

African (AFR) AF: 0.578 AC: 23946 AN: 41436

American (AMR) AF: 0.360 AC: 5494 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 785 AN: 3462

East Asian (EAS) AF: 0.666 AC: 3447 AN: 5172

South Asian (SAS) AF: 0.462 AC: 2224 AN: 4810

European-Finnish (FIN) AF: 0.383 AC: 4030 AN: 10512

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21502 AN: 67778

Other (OTH) AF: 0.405 AC: 851 AN: 2102

Alfa AF: 0.207 Hom.: 423

Bravo AF: 0.421

Asia WGS AF: 0.550 AC: 1908 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.30
PhyloP100		-0.24
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: rs4530574; hg19: chr4-5149387;