rs77177281
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_046105.1(MIR137HG):n.815-11146T>C 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 0.0247 in 152,158 control chromosomes in the GnomAD database, including 107 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 0.025 ( 107 hom., cov: 32)
Consequence
MIR137HG
NR_046105.1 intron, non_coding_transcript
NR_046105.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0550
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=-0.82).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0538 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR137HG | NR_046105.1 | n.815-11146T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR137HG | ENST00000602672.2 | n.141-26831T>C | intron_variant, non_coding_transcript_variant | 5 | |||||
MIR137HG | ENST00000424528.2 | n.985-11146T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
MIR137HG | ENST00000634594.1 | n.757-16577T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0248 AC: 3764AN: 152040Hom.: 107 Cov.: 32
GnomAD3 genomes
?
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3764
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152040
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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: 0.0247 AC: 3763AN: 152158Hom.: 107 Cov.: 32 AF XY: 0.0273 AC XY: 2032AN XY: 74400
GnomAD4 genome
?
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AC:
3763
AN:
152158
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32
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2032
AN XY:
74400
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71
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at