rs7100920

chr10-103881220-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• 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	UniProt
STN1	NM_024928.5	c.*1464G>A		3_prime_UTR_variant	10/10	ENST00000224950.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STN1	ENST00000224950.8	c.*1464G>A		3_prime_UTR_variant	10/10	1	NM_024928.5	P1

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

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.483

Alfa AF: 0.493 Hom.: 19117

Bravo AF: 0.471

Asia WGS AF: 0.372 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.7
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7100920; hg19: chr10-105640978;