dbSNP rs11191841: STN1:c.*2831A>G (chr10-103879853-T-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.*2831A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,198 control chromosomes in the GnomAD database, including 16,951 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 0.47 ( 16939 hom., cov: 33)

Exomes 𝑓: 0.46 ( 12 hom. )

Consequence

STN1
NM_024928.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.739

Publications

16 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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STN1	NM_024928.5 link	c.*2831A>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000224950.8	NP_079204.2	Q9H668

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STN1	ENST00000224950.8 link	c.*2831A>G		3_prime_UTR_variant	Exon 10 of 10	1	NM_024928.5	ENSP00000224950.3		Q9H668

Frequencies

GnomAD3 genomes

AF:

0.467

AC:

70906

AN:

151970

Hom.:

16934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.776

Gnomad AMR

AF:

0.504

Gnomad ASJ

AF:

0.415

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.601

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.502

Gnomad OTH

AF:

0.476

GnomAD4 exome

AF:

0.464

AC:

AN:

110

Hom.:

AF XY:

0.451

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.466

AC:

70921

AN:

152088

Hom.:

16939

Cov.:

AF XY:

0.470

AC XY:

34944

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.379

AC:

15721

AN:

41478

American (AMR)

AF:

0.505

AC:

7713

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.415

AC:

1436

AN:

3464

East Asian (EAS)

AF:

0.344

AC:

1776

AN:

5170

South Asian (SAS)

AF:

0.404

AC:

1945

AN:

4820

European-Finnish (FIN)

AF:

0.601

AC:

6353

AN:

10578

Middle Eastern (MID)

AF:

0.442

AC:

130

AN:

294

European-Non Finnish (NFE)

AF:

0.502

AC:

34139

AN:

67970

Other (OTH)

AF:

0.473

AC:

1000

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1976

3952

5929

7905

9881

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.480

Hom.:

8043

Bravo

AF:

0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.5

(source)

DANN

Benign

0.69

PhyloP100

-0.74

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs11191841

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