rs10420134
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001367856.1(PROSER3):c.*2481A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,044 control chromosomes in the GnomAD database, including 3,920 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 ( 3920 hom., cov: 32)
Exomes 𝑓: 0.33 ( 0 hom. )
Consequence
PROSER3
NM_001367856.1 3_prime_UTR
NM_001367856.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0800
Genes affected
PROSER3 (HGNC:25204): (proline and serine rich 3)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROSER3 | NM_001367856.1 | c.*2481A>G | 3_prime_UTR_variant | 11/11 | ENST00000646935.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROSER3 | ENST00000646935.2 | c.*2481A>G | 3_prime_UTR_variant | 11/11 | NM_001367856.1 | P3 | |||
PROSER3 | ENST00000396908.9 | c.*2481A>G | 3_prime_UTR_variant | 11/11 | 1 | A2 | |||
ENST00000589397.1 | n.3T>C | non_coding_transcript_exon_variant | 1/2 | 5 | |||||
PROSER3 | ENST00000544158.2 | n.1072A>G | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.221 AC: 33559AN: 151920Hom.: 3920 Cov.: 32
GnomAD3 genomes
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33559
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151920
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32
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GnomAD4 exome AF: 0.333 AC: 2AN: 6Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2AN XY: 4
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GnomAD4 genome ? AF: 0.221 AC: 33582AN: 152038Hom.: 3920 Cov.: 32 AF XY: 0.226 AC XY: 16809AN XY: 74322
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33582
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32
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3478
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