rs3813579
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000668946.1(MAFTRR):n.1931C>T 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 0.48 in 151,834 control chromosomes in the GnomAD database, including 17,839 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 0.48 ( 17839 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
MAFTRR
ENST00000668946.1 non_coding_transcript_exon
ENST00000668946.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.373
Genes affected
MAFTRR (HGNC:51525): (MAF transcriptional regulator RNA)
LINC01229 (HGNC:49682): (long intergenic non-protein coding RNA 1229)
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105371356 | XR_001752268.2 | n.746+492G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAFTRR | ENST00000668946.1 | n.1931C>T | non_coding_transcript_exon_variant | 6/6 | |||||
LINC01229 | ENST00000661087.1 | n.533+492G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.480 AC: 72807AN: 151716Hom.: 17846 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.480 AC: 72809AN: 151834Hom.: 17839 Cov.: 32 AF XY: 0.478 AC XY: 35443AN XY: 74208
GnomAD4 genome
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72809
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32
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1563
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3476
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