chr1-222628459-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198551.4(MIA3):c.1239A>T(p.Glu413Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,390 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198551.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIA3 | NM_198551.4 | c.1239A>T | p.Glu413Asp | missense_variant | 4/28 | ENST00000344922.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIA3 | ENST00000344922.10 | c.1239A>T | p.Glu413Asp | missense_variant | 4/28 | 5 | NM_198551.4 | P1 | |
MIA3 | ENST00000470521.1 | n.1251A>T | non_coding_transcript_exon_variant | 4/7 | 5 | ||||
MIA3 | ENST00000354906.7 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247254Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134134
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460144Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 726392
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1239A>T (p.E413D) alteration is located in exon 4 (coding exon 4) of the MIA3 gene. This alteration results from a A to T substitution at nucleotide position 1239, causing the glutamic acid (E) at amino acid position 413 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at