chr17-58270869-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000250.2(MPO):c.2031-6A>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,612,414 control chromosomes in the GnomAD database, including 19,702 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000250.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPO | NM_000250.2 | c.2031-6A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000225275.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPO | ENST00000225275.4 | c.2031-6A>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000250.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.150 AC: 22744AN: 151950Hom.: 1681 Cov.: 32
GnomAD3 exomes AF: 0.146 AC: 36548AN: 251030Hom.: 2762 AF XY: 0.149 AC XY: 20208AN XY: 135778
GnomAD4 exome AF: 0.156 AC: 227356AN: 1460346Hom.: 18017 Cov.: 32 AF XY: 0.157 AC XY: 113728AN XY: 726494
GnomAD4 genome ? AF: 0.150 AC: 22752AN: 152068Hom.: 1685 Cov.: 32 AF XY: 0.149 AC XY: 11098AN XY: 74344
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
MPO-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 17, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at