chr10-103879756-T-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024928.5(STN1):c.*2928A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 153,148 control chromosomes in the GnomAD database, including 9,104 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 0.33 ( 9005 hom., cov: 34)
Exomes 𝑓: 0.43 ( 99 hom. )
Consequence
STN1
NM_024928.5 3_prime_UTR
NM_024928.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.693
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STN1 | NM_024928.5 | c.*2928A>C | 3_prime_UTR_variant | 10/10 | ENST00000224950.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STN1 | ENST00000224950.8 | c.*2928A>C | 3_prime_UTR_variant | 10/10 | 1 | NM_024928.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.330 AC: 50229AN: 152022Hom.: 9006 Cov.: 34
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GnomAD4 exome AF: 0.428 AC: 431AN: 1008Hom.: 99 Cov.: 0 AF XY: 0.434 AC XY: 335AN XY: 772
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GnomAD4 genome ? AF: 0.330 AC: 50246AN: 152140Hom.: 9005 Cov.: 34 AF XY: 0.327 AC XY: 24318AN XY: 74368
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at