rs11997551
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001145860.2(POP1):c.-2-127A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 1,090,134 control chromosomes in the GnomAD database, including 104,333 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.43 ( 14570 hom., cov: 33)
Exomes 𝑓: 0.43 ( 89763 hom. )
Consequence
POP1
NM_001145860.2 intron
NM_001145860.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.964
Genes affected
POP1 (HGNC:30129): (POP1 homolog, ribonuclease P/MRP subunit) This gene encodes the protein subunit of two different small nucleolar ribonucleoprotein complexes: the endoribonuclease for mitochondrial RNA processing complex and the ribonuclease P complex. The encoded protein is a ribonuclease that localizes to the nucleus and functions in pre-RNA processing. This protein is also an autoantigen in patients suffering from connective tissue diseases. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 8-98123209-A-G is Benign according to our data. Variant chr8-98123209-A-G is described in ClinVar as [Benign]. Clinvar id is 1230258.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POP1 | NM_001145860.2 | c.-2-127A>G | intron_variant | ENST00000401707.7 | |||
POP1 | NM_001145861.2 | c.-2-127A>G | intron_variant | ||||
POP1 | NM_015029.3 | c.-2-127A>G | intron_variant | ||||
POP1 | XM_011516801.3 | c.-2-127A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POP1 | ENST00000401707.7 | c.-2-127A>G | intron_variant | 2 | NM_001145860.2 | P1 | |||
POP1 | ENST00000349693.3 | c.-2-127A>G | intron_variant | 1 | P1 | ||||
POP1 | ENST00000522319.5 | c.-2-127A>G | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.433 AC: 65875AN: 151980Hom.: 14560 Cov.: 33
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GnomAD4 exome AF: 0.433 AC: 406199AN: 938036Hom.: 89763 AF XY: 0.438 AC XY: 209619AN XY: 478376
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GnomAD4 genome ? AF: 0.433 AC: 65911AN: 152098Hom.: 14570 Cov.: 33 AF XY: 0.434 AC XY: 32243AN XY: 74358
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at