rs11191841

Positions:

• chr10-103879853-T-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

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]

ENSG00000289744 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
STN1	NM_024928.5	c.*2831A>G		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	c.*2831A>G		3_prime_UTR_variant	10/10	1	NM_024928.5	ENSP00000224950.3

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70906 AN: 151970 Hom.: 16934 Cov.: 33

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: 51 AN: 110 Hom.: 12 AF XY: 0.451 AC XY: 37 AN XY: 82

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.466 AC: 70921 AN: 152088 Hom.: 16939 Cov.: 33 AF XY: 0.470 AC XY: 34944 AN XY: 74360

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.473

Alfa AF: 0.483 Hom.: 6723

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
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11191841; hg19: chr10-105639611;