rs7910485

chr10-132235829-T-Cchr10-132235829-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173575.4(STK32C):c.319-7701A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,064 control chromosomes in the GnomAD database, including 41,723 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 0.74 (41723 hom., cov: 32)
• Consequence: STK32C NM_173575.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK32C	NM_173575.4	c.319-7701A>G		intron_variant		ENST00000298630.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK32C	ENST00000298630.8	c.319-7701A>G		intron_variant		1	NM_173575.4	P1
STK32C	ENST00000368622.5	c.-33-7701A>G		intron_variant		1
STK32C	ENST00000368620.2	c.358-7640A>G		intron_variant		3
STK32C	ENST00000462160.5	n.136-7701A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112399 AN: 151946 Hom.: 41685 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.740 AC: 112491 AN: 152064 Hom.: 41723 Cov.: 32 AF XY: 0.739 AC XY: 54914 AN XY: 74346

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.731

Alfa AF: 0.740 Hom.: 18919

Bravo AF: 0.747

Asia WGS AF: 0.652 AC: 2270 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	1.1
Dann	Benign	0.21

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: rs7910485; hg19: chr10-134049333;