dbSNP rs4387287: STN1:c.-102T>G (chr10-103918139-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024928.5(STN1):c.-102T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,622 control chromosomes in the GnomAD database, including 40,268 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 0.69 ( 40110 hom., cov: 33)

Exomes 𝑓: 0.80 ( 158 hom. )

Consequence

STN1
NM_024928.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.608

Publications

77 publications found

Variant links:

Genes affected

STN1 (HGNC:26200): (STN1 subunit of CST complex) OBFC1 and C17ORF68 (MIM 613129) are subunits of an alpha accessory factor (AAF) that stimulates the activity of DNA polymerase-alpha-primase (see MIM 176636), the enzyme that initiates DNA replication (Casteel et al., 2009 [PubMed 19119139]). OBFC1 also appears to function in a telomere-associated complex with C17ORF68 and TEN1 (C17ORF106; MIM 613130) (Miyake et al., 2009 [PubMed 19854130]).[supplied by OMIM, Nov 2009]

STN1 Gene-Disease associations (from GenCC):

cerebroretinal microangiopathy with calcifications and cysts 2
Inheritance: AR Classification: STRONG, MODERATE Submitted by: PanelApp Australia, G2P, Ambry Genetics, Genomics England PanelApp
Coats plus syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

STN1 links:

ENSG00000289744 (HGNC:):

ENSG00000289744 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STN1	NM_024928.5 link	c.-102T>G		5_prime_UTR_variant	Exon 1 of 10	ENST00000224950.8	NP_079204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STN1	ENST00000224950.8 link	c.-102T>G		5_prime_UTR_variant	Exon 1 of 10	1	NM_024928.5	ENSP00000224950.3

Frequencies

GnomAD3 genomes

AF:

0.694

AC:

105558

AN:

152010

Hom.:

40109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.354

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.766

Gnomad ASJ

AF:

0.797

Gnomad EAS

AF:

0.825

Gnomad SAS

AF:

0.808

Gnomad FIN

AF:

0.861

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.832

Gnomad OTH

AF:

0.719

GnomAD4 exome

AF:

0.800

AC:

395

AN:

494

Hom.:

158

Cov.:

AF XY:

0.799

AC XY:

294

AN XY:

368

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.714

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.826

AC:

119

AN:

144

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.667

AC:

AN:

European-Non Finnish (NFE)

AF:

0.804

AC:

246

AN:

306

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.694

AC:

105567

AN:

152128

Hom.:

40110

Cov.:

AF XY:

0.699

AC XY:

52014

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.353

AC:

14655

AN:

41470

American (AMR)

AF:

0.766

AC:

11721

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.797

AC:

2765

AN:

3468

East Asian (EAS)

AF:

0.825

AC:

4254

AN:

5158

South Asian (SAS)

AF:

0.809

AC:

3903

AN:

4826

European-Finnish (FIN)

AF:

0.861

AC:

9130

AN:

10606

Middle Eastern (MID)

AF:

0.765

AC:

225

AN:

294

European-Non Finnish (NFE)

AF:

0.832

AC:

56548

AN:

67984

Other (OTH)

AF:

0.714

AC:

1509

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1328

2655

3983

5310

6638

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

804

1608

2412

3216

4020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.806

Hom.:

100603

Bravo

AF:

0.673

Asia WGS

AF:

0.750

AC:

2609

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.4

(source)

DANN

Benign

0.49

PhyloP100

0.61

PromoterAI

0.081

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over