rs4553158
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001077700.3(MIER1):c.773-45A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,393,584 control chromosomes in the GnomAD database, including 18,907 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 0.12 ( 1471 hom., cov: 32)
Exomes 𝑓: 0.16 ( 17436 hom. )
Consequence
MIER1
NM_001077700.3 intron
NM_001077700.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.62
Genes affected
MIER1 (HGNC:29657): (MIER1 transcriptional regulator) This gene encodes a protein that was first identified in Xenopus laevis by its role in a mesoderm induction early response (MIER). The encoded protein functions as a transcriptional regulator. Alternatively spliced transcript variants encode multiple isoforms, some of which lack a C-terminal nuclear localization signal. [provided by RefSeq, May 2013]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIER1 | NM_001077700.3 | c.773-45A>G | intron_variant | ENST00000401041.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIER1 | ENST00000401041.6 | c.773-45A>G | intron_variant | 2 | NM_001077700.3 |
Frequencies
GnomAD3 genomes ? AF: 0.122 AC: 18481AN: 152048Hom.: 1474 Cov.: 32
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GnomAD3 exomes AF: 0.144 AC: 22602AN: 157038Hom.: 1920 AF XY: 0.147 AC XY: 12525AN XY: 85288
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GnomAD4 exome AF: 0.162 AC: 201495AN: 1241418Hom.: 17436 Cov.: 17 AF XY: 0.161 AC XY: 98901AN XY: 615156
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GnomAD4 genome ? AF: 0.121 AC: 18474AN: 152166Hom.: 1471 Cov.: 32 AF XY: 0.122 AC XY: 9094AN XY: 74408
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at