rs7100920

Variant names:

• chr10-103881220-C-T
• rs7100920
• NM_024928.5:c.*1464G>A

Variant summary

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

The NM_024928.5(STN1):​c.*1464G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,078 control chromosomes in the GnomAD database, including 17,617 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 0.48 (17617 hom., cov: 33)
• Consequence: STN1 NM_024928.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 20 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: G2P, Ambry Genetics, Genomics England PanelApp, PanelApp Australia
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024928.5. 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
	STN1	NM_024928.5	MANE Select	c.*1464G>A		3_prime_UTR	Exon 10 of 10	NP_079204.2	Q9H668

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STN1	ENST00000224950.8	TSL:1 MANE Select	c.*1464G>A		3_prime_UTR	Exon 10 of 10	ENSP00000224950.3	Q9H668
	STN1	ENST00000369764.2	TSL:2	c.*1464G>A		3_prime_UTR	Exon 9 of 9	ENSP00000358779.1	Q9H668
	STN1	ENST00000698243.1		c.*1464G>A		3_prime_UTR	Exon 10 of 10	ENSP00000513623.1	Q9H668

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72750 AN: 151958 Hom.: 17614 Cov.: 33

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.479 AC: 72772 AN: 152078 Hom.: 17617 Cov.: 33 AF XY: 0.482 AC XY: 35804 AN XY: 74336

African (AFR) AF: 0.431 AC: 17868 AN: 41478

American (AMR) AF: 0.508 AC: 7760 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3472

East Asian (EAS) AF: 0.344 AC: 1776 AN: 5170

South Asian (SAS) AF: 0.403 AC: 1946 AN: 4826

European-Finnish (FIN) AF: 0.600 AC: 6340 AN: 10564

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33846 AN: 67974

Other (OTH) AF: 0.483 AC: 1019 AN: 2108

Alfa AF: 0.490 Hom.: 24317

Bravo AF: 0.471

Asia WGS AF: 0.372 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.61
PhyloP100		0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7100920;

hg19: chr10-105640978;