10-132220875-A-G

Variant names:

• chr10-132220875-A-G
• rs2035804
• NM_173575.4:c.1251+1766T>C

Variant summary

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

The NM_001318878.2(STK32C):​c.1290+1766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,148 control chromosomes in the GnomAD database, including 46,540 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 0.78 (46540 hom., cov: 32)
• Consequence: STK32C NM_001318878.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 11 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318878.2. 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
	STK32C	NM_173575.4	MANE Select	c.1251+1766T>C		intron	N/A	NP_775846.2
	STK32C	NM_001318878.2		c.1290+1766T>C		intron	N/A	NP_001305807.1
	STK32C	NM_001318879.2		c.900+1766T>C		intron	N/A	NP_001305808.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32C	ENST00000298630.8	TSL:1 MANE Select	c.1251+1766T>C		intron	N/A	ENSP00000298630.3
	STK32C	ENST00000368622.5	TSL:1	c.900+1766T>C		intron	N/A	ENSP00000357611.1
	STK32C	ENST00000916800.1		c.1275+1766T>C		intron	N/A	ENSP00000586859.1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118573 AN: 152030 Hom.: 46498 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.780 AC: 118677 AN: 152148 Hom.: 46540 Cov.: 32 AF XY: 0.782 AC XY: 58164 AN XY: 74404

African (AFR) AF: 0.711 AC: 29485 AN: 41456

American (AMR) AF: 0.854 AC: 13062 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2521 AN: 3468

East Asian (EAS) AF: 0.853 AC: 4418 AN: 5180

South Asian (SAS) AF: 0.759 AC: 3652 AN: 4812

European-Finnish (FIN) AF: 0.791 AC: 8392 AN: 10608

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54425 AN: 68006

Other (OTH) AF: 0.784 AC: 1655 AN: 2112

Alfa AF: 0.791 Hom.: 78832

Bravo AF: 0.784

Asia WGS AF: 0.770 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-0.50
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: rs2035804; hg19: chr10-134034379;