rs755622
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_038911(MIF-AS1):n.1697C>G 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 0.254 in 152146 control chromosomes in the gnomAD Genomes database, including 5790 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.25 ( 5790 hom., cov: 34)
Consequence
MIF-AS1
NR_038911 non_coding_transcript_exon
NR_038911 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.948
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIF-AS1 | NR_038911.1 | n.1697C>G | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38654AN: 152146Hom.: 5790 Cov.: 34
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GnomAD4 exome AF: 0.192 AC: 81356AN: 423348Hom.: 8518 AF XY: 0.194 AC XY: 43705AN XY: 225798
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ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Rheumatoid arthritis, systemic juvenile, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | May 01, 2003 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at