10-132274486-A-G

Position:

• chr10-132274486-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
STK32C	NM_173575.4	c.263-28531T>C		intron_variant		ENST00000298630.8	NP_775846.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK32C	ENST00000298630.8	c.263-28531T>C		intron_variant		1	NM_173575.4	ENSP00000298630	P1
STK32C	ENST00000368622.5	c.-89-28531T>C		intron_variant		1		ENSP00000357611
STK32C	ENST00000368620.2	c.302-28531T>C		intron_variant		3		ENSP00000357609

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

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.0693

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.413

Alfa AF: 0.400 Hom.: 25155

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

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: rs11146301; hg19: chr10-134087990;