1-222628226-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198551.4(MIA3):c.1006G>A(p.Gly336Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,614,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_198551.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIA3 | NM_198551.4 | c.1006G>A | p.Gly336Arg | missense_variant | 4/28 | ENST00000344922.10 | NP_940953.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIA3 | ENST00000344922.10 | c.1006G>A | p.Gly336Arg | missense_variant | 4/28 | 5 | NM_198551.4 | ENSP00000340900.5 | ||
MIA3 | ENST00000470521.1 | n.1018G>A | non_coding_transcript_exon_variant | 4/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 249034Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135176
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461788Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 727188
GnomAD4 genome AF: 0.000256 AC: 39AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74480
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2024 | The c.1006G>A (p.G336R) alteration is located in exon 4 (coding exon 4) of the MIA3 gene. This alteration results from a G to A substitution at nucleotide position 1006, causing the glycine (G) at amino acid position 336 to be replaced by an arginine (R). 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