rs10516153
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_024617.1(PART1):n.712-5370C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0855 in 152,372 control chromosomes in the GnomAD database, including 1,611 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 0.086 ( 1611 hom., cov: 32)
Exomes 𝑓: 0.024 ( 0 hom. )
Consequence
PART1
NR_024617.1 intron, non_coding_transcript
NR_024617.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.109
Genes affected
PART1 (HGNC:17263): (prostate androgen-regulated transcript 1) This gene is induced by androgen in prostate adenocarcinoma cells. Multiple alternatively transcript variants have been described for this gene, none of which are predicted to encode a protein product. [provided by RefSeq, Sep 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=-0.82).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PART1 | NR_024617.1 | n.712-5370C>T | intron_variant, non_coding_transcript_variant | ||||
PART1 | NR_028509.1 | n.3507C>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PART1 | ENST00000506884.2 | n.301-5370C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0854 AC: 12982AN: 152090Hom.: 1597 Cov.: 32
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GnomAD4 exome AF: 0.0244 AC: 4AN: 164Hom.: 0 Cov.: 0 AF XY: 0.0400 AC XY: 4AN XY: 100
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GnomAD4 genome ? AF: 0.0856 AC: 13031AN: 152208Hom.: 1611 Cov.: 32 AF XY: 0.0828 AC XY: 6167AN XY: 74438
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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