rs135771
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_110522.2(MIR3667HG):n.115+113869C>T 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 154,486 control chromosomes in the GnomAD database, including 2,484 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 ( 2464 hom., cov: 32)
Exomes 𝑓: 0.10 ( 20 hom. )
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: -0.281
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=-1.0).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR3667HG | NR_110522.2 | n.115+113869C>T | intron_variant, non_coding_transcript_variant | ||||
MIR3667HG | NR_110523.2 | n.116-102324C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR3667HG | ENST00000414287.5 | n.101-102324C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
MIR3667HG | ENST00000416411.1 | n.54-102324C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24514AN: 151866Hom.: 2463 Cov.: 32
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GnomAD4 exome AF: 0.102 AC: 255AN: 2502Hom.: 20 AF XY: 0.0997 AC XY: 128AN XY: 1284
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GnomAD4 genome ? AF: 0.162 AC: 24546AN: 151984Hom.: 2464 Cov.: 32 AF XY: 0.159 AC XY: 11835AN XY: 74304
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at