rs2492651

Variant names:

• chr10-132304496-C-T
• rs2492651
• NM_173575.4:c.262+3076G>A

Variant summary

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

The NM_173575.4(STK32C):​c.262+3076G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,154 control chromosomes in the GnomAD database, including 53,460 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 0.83 (53460 hom., cov: 31)
• Consequence: STK32C NM_173575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK32C	NM_173575.4	c.262+3076G>A		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.262+3076G>A		intron_variant	Intron 1 of 11	1	NM_173575.4	ENSP00000298630.3
STK32C	ENST00000368622.5	c.-90+2426G>A		intron_variant	Intron 1 of 11	1		ENSP00000357611.1
STK32C	ENST00000368620.2	c.301+26940G>A		intron_variant	Intron 1 of 3	3		ENSP00000357609.3

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126561 AN: 152036 Hom.: 53393 Cov.: 31

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.833 AC: 126690 AN: 152154 Hom.: 53460 Cov.: 31 AF XY: 0.833 AC XY: 61987 AN XY: 74386

African (AFR) AF: 0.959 AC: 39850 AN: 41540

American (AMR) AF: 0.866 AC: 13242 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3150 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4566 AN: 5164

South Asian (SAS) AF: 0.821 AC: 3950 AN: 4814

European-Finnish (FIN) AF: 0.732 AC: 7737 AN: 10568

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51304 AN: 67988

Other (OTH) AF: 0.844 AC: 1784 AN: 2114

Alfa AF: 0.787 Hom.: 77913

Bravo AF: 0.850

Asia WGS AF: 0.843 AC: 2931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.62
PhyloP100		-0.38
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: rs2492651; hg19: chr10-134118000;