rs925114
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_011521392.2(MINAR1):c.-431A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,088 control chromosomes in the GnomAD database, including 14,297 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 0.43 ( 14293 hom., cov: 32)
Exomes 𝑓: 0.75 ( 4 hom. )
Consequence
MINAR1
XM_011521392.2 5_prime_UTR
XM_011521392.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.240
Genes affected
TMED3 (HGNC:28889): (transmembrane p24 trafficking protein 3) Predicted to be involved in Golgi organization; endoplasmic reticulum to Golgi vesicle-mediated transport; and intracellular protein transport. Located in Golgi apparatus; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MINAR1 | XM_011521392.2 | c.-431A>G | 5_prime_UTR_variant | 1/4 | |||
TMED3 | NM_001330376.2 | c.*1673A>G | 3_prime_UTR_variant | 3/3 | |||
MINAR1 | XM_017022027.2 | c.-51+1537A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMED3 | ENST00000424155.6 | c.*1673A>G | 3_prime_UTR_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.427 AC: 64912AN: 151958Hom.: 14291 Cov.: 32
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151958
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32
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GnomAD4 exome AF: 0.750 AC: 9AN: 12Hom.: 4 Cov.: 0 AF XY: 0.700 AC XY: 7AN XY: 10
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GnomAD4 genome ? AF: 0.427 AC: 64918AN: 152076Hom.: 14293 Cov.: 32 AF XY: 0.421 AC XY: 31276AN XY: 74334
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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
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at