rs2902638

Positions:

• chr10-103877231-T-C

Variant summary

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

The ENST00000698241.1(STN1):​c.*39+5414A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,246 control chromosomes in the GnomAD database, including 3,820 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 0.22 (3820 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: STN1 ENST00000698241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STN1	ENST00000698241.1	c.*39+5414A>G		intron_variant				P1
STN1	ENST00000698242.1	c.*39+5414A>G		intron_variant				P1
STN1	ENST00000698297.1	c.*39+5414A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32808 AN: 152128 Hom.: 3818 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.216 AC: 32816 AN: 152246 Hom.: 3820 Cov.: 33 AF XY: 0.218 AC XY: 16242 AN XY: 74426

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.218

Alfa AF: 0.244 Hom.: 9323

Bravo AF: 0.206

Asia WGS AF: 0.205 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	17
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2902638; hg19: chr10-105636989;