rs5770418
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_110522.2(MIR3667HG):n.116-1499G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,040 control chromosomes in the GnomAD database, including 1,962 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 0.16 ( 1962 hom., cov: 32)
Consequence
MIR3667HG
NR_110522.2 intron, non_coding_transcript
NR_110522.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.20
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=-0.93).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR3667HG | NR_110522.2 | n.116-1499G>A | intron_variant, non_coding_transcript_variant | ||||
MIR3667HG | NR_110523.2 | n.453-1499G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR3667HG | ENST00000414287.5 | n.438-1499G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
MIR3667HG | ENST00000498829.1 | n.368-1499G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24423AN: 151922Hom.: 1950 Cov.: 32
GnomAD3 genomes
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24423
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.161 AC: 24465AN: 152040Hom.: 1962 Cov.: 32 AF XY: 0.160 AC XY: 11894AN XY: 74298
GnomAD4 genome
?
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24465
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152040
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32
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11894
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74298
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620
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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