rs2758357
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000403291.1(HNRNPH1P1):n.27G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 790,188 control chromosomes in the GnomAD database, including 67,318 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 0.40 ( 13691 hom., cov: 30)
Exomes 𝑓: 0.39 ( 53627 hom. )
Consequence
HNRNPH1P1
ENST00000403291.1 non_coding_transcript_exon
ENST00000403291.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0620
Genes affected
HNRNPH1P1 (HGNC:48751): (heterogeneous nuclear ribonucleoprotein H1 pseudogene 1)
SOD2 (HGNC:11180): (superoxide dismutase 2) This gene is a member of the iron/manganese superoxide dismutase family. It encodes a mitochondrial protein that forms a homotetramer and binds one manganese ion per subunit. This protein binds to the superoxide byproducts of oxidative phosphorylation and converts them to hydrogen peroxide and diatomic oxygen. Mutations in this gene have been associated with idiopathic cardiomyopathy (IDC), premature aging, sporadic motor neuron disease, and cancer. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 1. [provided by RefSeq, Apr 2016]
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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=-0.65).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOD2 | NM_001322817.2 | c.-116+16926G>A | intron_variant | ||||
SOD2 | NM_001322819.2 | c.-116+13307G>A | intron_variant | ||||
SOD2 | NM_001322820.2 | c.-116+12893G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNRNPH1P1 | ENST00000403291.1 | n.27G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.404 AC: 61277AN: 151674Hom.: 13684 Cov.: 30
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GnomAD4 exome AF: 0.390 AC: 248900AN: 638396Hom.: 53627 Cov.: 8 AF XY: 0.396 AC XY: 132096AN XY: 333888
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GnomAD4 genome ? AF: 0.404 AC: 61279AN: 151792Hom.: 13691 Cov.: 30 AF XY: 0.402 AC XY: 29847AN XY: 74158
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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