chr10-103909864-T-C

Position:

• chr10-103909864-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.229+663A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,986 control chromosomes in the GnomAD database, including 15,752 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 0.45 (15752 hom., cov: 31)
• Consequence: STN1 NM_024928.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STN1	NM_024928.5	c.229+663A>G		intron_variant		ENST00000224950.8	NP_079204.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STN1	ENST00000224950.8	c.229+663A>G		intron_variant		1	NM_024928.5	ENSP00000224950	P1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67627 AN: 151868 Hom.: 15747 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.445 AC: 67643 AN: 151986 Hom.: 15752 Cov.: 31 AF XY: 0.449 AC XY: 33353 AN XY: 74290

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.457

Alfa AF: 0.457 Hom.: 3075

Bravo AF: 0.433

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.70

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: rs12765878; hg19: chr10-105669622;