rs911547

Positions:

• chr10-103879663-G-A
• chr10-103879663-G-C
• chr10-103879663-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024928.5(STN1):​c.*3021C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,682 control chromosomes in the GnomAD database, including 45,802 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 0.76 (45603 hom., cov: 33)
  • Exomes 𝑓: 0.86 (199 hom.)
• Consequence: STN1 NM_024928.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STN1	NM_024928.5	c.*3021C>T		3_prime_UTR_variant	10/10	ENST00000224950.8	NP_079204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STN1	ENST00000224950.8	c.*3021C>T		3_prime_UTR_variant	10/10	1	NM_024928.5	ENSP00000224950	P1

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115046 AN: 152030 Hom.: 45603 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.774

GnomAD4 exome AF: 0.861 AC: 458 AN: 532 Hom.: 199 Cov.: 0 AF XY: 0.868 AC XY: 335 AN XY: 386

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.906

Gnomad4 NFE exome AF: 0.853

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.756 AC: 115071 AN: 152150 Hom.: 45603 Cov.: 33 AF XY: 0.763 AC XY: 56720 AN XY: 74384

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.770

Alfa AF: 0.830 Hom.: 58582

Bravo AF: 0.744

Asia WGS AF: 0.854 AC: 2972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs911547; hg19: chr10-105639421;