rs1411340638

Variant names:

• chr10-68827853-C-G
• rs1411340638
• NM_152709.5:c.230C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-68827853-C-G
• chr10-68827853-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_152709.5(STOX1):​c.230C>G​(p.Pro77Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P77L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 7)
  • Failed GnomAD Quality Control
• Consequence: STOX1 NM_152709.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0670
• Publications: 0 publications found

Genes affected

STOX1 (HGNC:23508): (storkhead box 1) Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including positive regulation of G2/M transition of mitotic cell cycle; positive regulation of protein phosphorylation; and regulation of gene expression. Located in centrosome; cytosol; and nuclear lumen. Implicated in pre-eclampsia. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.23896018).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152709.5. 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
	STOX1	NM_152709.5	MANE Select	c.230C>G	p.Pro77Arg	missense	Exon 1 of 4	NP_689922.3
	STOX1	NM_001130161.4		c.230C>G	p.Pro77Arg	missense	Exon 1 of 5	NP_001123633.1	Q6ZVD7-1
	STOX1	NM_001130159.3		c.230C>G	p.Pro77Arg	missense	Exon 1 of 4	NP_001123631.1	Q6ZVD7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STOX1	ENST00000298596.11	TSL:1 MANE Select	c.230C>G	p.Pro77Arg	missense	Exon 1 of 4	ENSP00000298596.6	Q6ZVD7-1
	STOX1	ENST00000399169.8	TSL:1	c.230C>G	p.Pro77Arg	missense	Exon 1 of 5	ENSP00000382121.4	Q6ZVD7-1
	STOX1	ENST00000399165.8	TSL:1	c.230C>G	p.Pro77Arg	missense	Exon 1 of 4	ENSP00000382118.4	Q6ZVD7-2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 55660 Hom.: 0 Cov.: 7

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 4

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 55660 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 27502

African (AFR) AF: 0.00 AC: 0 AN: 13720

American (AMR) AF: 0.00 AC: 0 AN: 7416

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1460

East Asian (EAS) AF: 0.00 AC: 0 AN: 1492

South Asian (SAS) AF: 0.00 AC: 0 AN: 1418

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3492

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 158

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 25756

Other (OTH) AF: 0.00 AC: 0 AN: 636

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Uncertain	0.032	T
BayesDel_noAF	Benign	-0.19
CADD	Benign	15
DANN	Uncertain	0.97
DEOGEN2	Benign	0.086	T
Eigen	Benign	-0.58
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.034	N
LIST_S2	Benign	0.57	T
M_CAP	Pathogenic	0.99	D
MetaRNN	Benign	0.24	T
MetaSVM	Benign	-0.53	T
MutationAssessor	Benign	1.6	L
PhyloP100		0.067
PROVEAN	Uncertain	-2.4	N
REVEL	Benign	0.19
Sift	Benign	0.031	D
Sift4G	Benign	0.10	T
Polyphen		0.72	P
Vest4		0.24
MutPred		0.45		Loss of loop (P = 0.0075)
MVP		0.49
MPC		0.24
ClinPred		0.30	T
GERP RS		1.9
PromoterAI		0.058	Neutral
Varity_R		0.10
gMVP		0.12
Mutation Taster		=88/12	polymorphism

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: rs1411340638; hg19: chr10-70587610;