rs7910485

Variant names:

• chr10-132235829-T-C
• rs7910485
• NM_173575.4:c.319-7701A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-132235829-T-C
• chr10-132235829-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173575.4. 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.319-7701A>G		intron	N/A	NP_775846.2
	STK32C	NM_001318878.2		c.358-7701A>G		intron	N/A	NP_001305807.1	B7Z7J1
	STK32C	NM_001318879.2		c.-33-7701A>G		intron	N/A	NP_001305808.1	Q86UX6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK32C	ENST00000298630.8	TSL:1 MANE Select	c.319-7701A>G		intron	N/A	ENSP00000298630.3	Q86UX6-1
	STK32C	ENST00000368622.5	TSL:1	c.-33-7701A>G		intron	N/A	ENSP00000357611.1	Q86UX6-2
	STK32C	ENST00000916800.1		c.319-7701A>G		intron	N/A	ENSP00000586859.1

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

African (AFR) AF: 0.717 AC: 29744 AN: 41458

American (AMR) AF: 0.797 AC: 12187 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3472

East Asian (EAS) AF: 0.672 AC: 3467 AN: 5160

South Asian (SAS) AF: 0.655 AC: 3153 AN: 4814

European-Finnish (FIN) AF: 0.737 AC: 7794 AN: 10572

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

European-Non Finnish (NFE) AF: 0.748 AC: 50884 AN: 67986

Other (OTH) AF: 0.731 AC: 1539 AN: 2104

Alfa AF: 0.742 Hom.: 21124

Bravo AF: 0.747

Asia WGS AF: 0.652 AC: 2270 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	1.1
DANN	Benign	0.21
PhyloP100		-2.8
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: rs7910485; hg19: chr10-134049333;