chr2-111366168-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000451884.6(MIR4435-2HG):n.215A>C 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 0.00205 in 152,322 control chromosomes in the GnomAD database, including 6 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 0.0021 ( 6 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MIR4435-2HG
ENST00000451884.6 non_coding_transcript_exon
ENST00000451884.6 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.45
Genes affected
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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=-0.72).
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00205 (313/152322) while in subpopulation EAS AF= 0.0209 (108/5174). AF 95% confidence interval is 0.0177. There are 6 homozygotes in gnomad4. There are 197 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIR4435-2HG | ENST00000439362.6 | n.273+1319A>C | intron_variant | 1 | ||||||
MIR4435-2HG | ENST00000451884.6 | n.215A>C | non_coding_transcript_exon_variant | 1/5 | 3 | |||||
MIR4435-2HG | ENST00000643013.1 | n.1644A>C | non_coding_transcript_exon_variant | 2/6 |
Frequencies
GnomAD3 genomes AF: 0.00206 AC: 314AN: 152204Hom.: 6 Cov.: 30
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 36Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 26
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GnomAD4 genome AF: 0.00205 AC: 313AN: 152322Hom.: 6 Cov.: 30 AF XY: 0.00265 AC XY: 197AN XY: 74472
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at