rs7944477
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_120571.1(MIR4300HG):n.941-22885G>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 0.0708 in 152,032 control chromosomes in the GnomAD database, including 562 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 0.071 ( 562 hom., cov: 32)
Consequence
MIR4300HG
NR_120571.1 intron, non_coding_transcript
NR_120571.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.620
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=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR4300HG | NR_120571.1 | n.941-22885G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIR4300HG | ENST00000500502.5 | n.941-22885G>T | intron_variant, non_coding_transcript_variant | 1 | |||||
MIR4300HG | ENST00000530896.6 | n.473-22885G>T | intron_variant, non_coding_transcript_variant | 3 | |||||
MIR4300HG | ENST00000653173.1 | n.419-80250G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0706 AC: 10728AN: 151914Hom.: 557 Cov.: 32
GnomAD3 genomes
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10728
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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: 0.0708 AC: 10759AN: 152032Hom.: 562 Cov.: 32 AF XY: 0.0679 AC XY: 5050AN XY: 74344
GnomAD4 genome
?
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10759
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32
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5050
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74344
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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