10-103875137-G-A

Variant names:

• chr10-103875137-G-A
• rs11191839
• ENST00000698241.1:c.*40-4243C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000698241.1(STN1):​c.*40-4243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,036 control chromosomes in the GnomAD database, including 7,982 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 0.30 (7982 hom., cov: 33)
• Consequence: STN1 ENST00000698241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 16 publications found

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

ENSG00000289744 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000698241.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STN1	ENST00000698241.1		c.*40-4243C>T		intron	N/A	ENSP00000513621.1
	STN1	ENST00000698242.1		c.*40-4243C>T		intron	N/A	ENSP00000513622.1
	STN1	ENST00000698297.1		c.*39+7508C>T		intron	N/A	ENSP00000513657.1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45872 AN: 151916 Hom.: 7973 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.302 AC: 45889 AN: 152036 Hom.: 7982 Cov.: 33 AF XY: 0.303 AC XY: 22519 AN XY: 74320

African (AFR) AF: 0.148 AC: 6128 AN: 41530

American (AMR) AF: 0.341 AC: 5216 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3466

East Asian (EAS) AF: 0.648 AC: 3328 AN: 5136

South Asian (SAS) AF: 0.498 AC: 2403 AN: 4824

European-Finnish (FIN) AF: 0.244 AC: 2583 AN: 10584

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23865 AN: 67904

Other (OTH) AF: 0.308 AC: 650 AN: 2112

Alfa AF: 0.342 Hom.: 14647

Bravo AF: 0.303

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.59
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs11191839; hg19: chr10-105634895;