rs10800597
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000436880.2(MIR181A1HG):n.1819C>T 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 0.724 in 151,930 control chromosomes in the GnomAD database, including 40,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.72 ( 40351 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
MIR181A1HG
ENST00000436880.2 non_coding_transcript_exon
ENST00000436880.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.819
Genes affected
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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=-0.86).
BP6
?
Variant 1-198898955-G-A is Benign according to our data. Variant chr1-198898955-G-A is described in ClinVar as [Benign]. Clinvar id is 427755.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR181A1HG | NR_040073.1 | n.363+1456C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR181A1HG | ENST00000660348.1 | n.355+1456C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.724 AC: 109963AN: 151812Hom.: 40313 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.724 AC: 110059AN: 151930Hom.: 40351 Cov.: 32 AF XY: 0.730 AC XY: 54176AN XY: 74210
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ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Acute myeloblastic leukemia with maturation Pathogenic:1
Pathogenic, no assertion criteria provided | case-control | Fujian Institute of Hematology, Fujian Medical University | - | This variant contributes to development of AML-M2 - |
not specified Benign:1
Benign, criteria provided, single submitter | research | H3Africa Consortium | Oct 28, 2020 | While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.875, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. - |
Computational 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