rs4387287

chr10-103918139-A-Cchr10-103918139-A-G

Variant summary

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

The NM_024928.5(STN1):c.-102T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,622 control chromosomes in the GnomAD database, including 40,268 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 0.69 (40110 hom., cov: 33)
  • Exomes 𝑓: 0.80 (158 hom.)
• Consequence: STN1 NM_024928.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STN1	NM_024928.5	c.-102T>G		5_prime_UTR_variant	1/10	ENST00000224950.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STN1	ENST00000224950.8	c.-102T>G		5_prime_UTR_variant	1/10	1	NM_024928.5	P1

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105558 AN: 152010 Hom.: 40109 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.719

GnomAD4 exome AF: 0.800 AC: 395 AN: 494 Hom.: 158 Cov.: 0 AF XY: 0.799 AC XY: 294 AN XY: 368

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.714

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.826

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.804

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.694 AC: 105567 AN: 152128 Hom.: 40110 Cov.: 33 AF XY: 0.699 AC XY: 52014 AN XY: 74376

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.714

Alfa AF: 0.811 Hom.: 71500

Bravo AF: 0.673

Asia WGS AF: 0.750 AC: 2609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.4
Dann	Benign	0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4387287; hg19: chr10-105677897;