rs10737190
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022114.4(PRDM16):c.387+5458G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,208 control chromosomes in the GnomAD database, including 61,866 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 0.90 ( 61866 hom., cov: 31)
Consequence
PRDM16
NM_022114.4 intron
NM_022114.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.25
Genes affected
PRDM16 (HGNC:14000): (PR/SET domain 16) The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal PR domain. The translocation results in the overexpression of a truncated version of this protein that lacks the PR domain, which may play an important role in the pathogenesis of MDS and AML. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM16 | NM_022114.4 | c.387+5458G>A | intron_variant | ENST00000270722.10 | |||
LOC107984909 | XR_001737869.2 | n.4375G>A | non_coding_transcript_exon_variant | 1/2 | |||
PRDM16 | NM_199454.3 | c.387+5458G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM16 | ENST00000270722.10 | c.387+5458G>A | intron_variant | 1 | NM_022114.4 | P1 | |||
PRDM16 | ENST00000378391.6 | c.387+5458G>A | intron_variant | 1 | |||||
PRDM16 | ENST00000511072.5 | c.387+5458G>A | intron_variant | 5 | |||||
PRDM16 | ENST00000514189.5 | c.387+5458G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.901 AC: 137059AN: 152090Hom.: 61840 Cov.: 31
GnomAD3 genomes
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GnomAD4 genome ? AF: 0.901 AC: 137133AN: 152208Hom.: 61866 Cov.: 31 AF XY: 0.901 AC XY: 67044AN XY: 74416
GnomAD4 genome
?
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2982
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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
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at