17-18263764-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_139162.4(MIEF2):c.365C>T(p.Pro122Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,607,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_139162.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIEF2 | NM_139162.4 | c.365C>T | p.Pro122Leu | missense_variant | 4/4 | ENST00000323019.9 | NP_631901.2 | |
MIEF2 | NM_148886.2 | c.398C>T | p.Pro133Leu | missense_variant | 4/4 | NP_683684.2 | ||
MIEF2 | XM_017024190.2 | c.386C>T | p.Pro129Leu | missense_variant | 4/4 | XP_016879679.1 | ||
MIEF2 | NM_001144900.3 | c.311-20C>T | intron_variant | NP_001138372.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000606 AC: 15AN: 247370Hom.: 0 AF XY: 0.0000670 AC XY: 9AN XY: 134366
GnomAD4 exome AF: 0.0000261 AC: 38AN: 1455256Hom.: 0 Cov.: 30 AF XY: 0.0000235 AC XY: 17AN XY: 723082
GnomAD4 genome AF: 0.000112 AC: 17AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74360
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | MIEF2: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at