10-132274486-A-G

Variant names:

• chr10-132274486-A-G
• rs11146301
• NM_173575.4:c.263-28531T>C

Variant summary

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

The NM_173575.4(STK32C):​c.263-28531T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,102 control chromosomes in the GnomAD database, including 15,364 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 0.43 (15364 hom., cov: 33)
• Consequence: STK32C NM_173575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 6 publications found

Genes affected

STK32C (HGNC:21332): (serine/threonine kinase 32C) The protein encoded by this gene is a member of the serine/threonine protein kinase family. It is thought that this family member is functional in brain due to its high expression levels there. DNA methylation differences have been found in this gene in monozygotic twins that are discordant for adolescent depression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK32C	NM_173575.4	c.263-28531T>C		intron_variant	Intron 1 of 11	ENST00000298630.8	NP_775846.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK32C	ENST00000298630.8	c.263-28531T>C		intron_variant	Intron 1 of 11	1	NM_173575.4	ENSP00000298630.3
STK32C	ENST00000368622.5	c.-89-28531T>C		intron_variant	Intron 1 of 11	1		ENSP00000357611.1
STK32C	ENST00000368620.2	c.302-28531T>C		intron_variant	Intron 1 of 3	3		ENSP00000357609.3

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65753 AN: 151984 Hom.: 15335 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.433 AC: 65831 AN: 152102 Hom.: 15364 Cov.: 33 AF XY: 0.423 AC XY: 31459 AN XY: 74348

African (AFR) AF: 0.596 AC: 24695 AN: 41460

American (AMR) AF: 0.343 AC: 5241 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1418 AN: 3472

East Asian (EAS) AF: 0.0693 AC: 359 AN: 5178

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4822

European-Finnish (FIN) AF: 0.301 AC: 3187 AN: 10582

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27935 AN: 67986

Other (OTH) AF: 0.413 AC: 873 AN: 2112

Alfa AF: 0.411 Hom.: 56662

Bravo AF: 0.442

Asia WGS AF: 0.221 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.36
PhyloP100		-0.23
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: rs11146301; hg19: chr10-134087990;