chr17-18263105-G-A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_139162.4(MIEF2):c.167G>A(p.Ser56Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000265 in 1,613,318 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 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
Publications
- combined oxidative phosphorylation deficiency 49Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIEF2 | NM_139162.4 | c.167G>A | p.Ser56Asn | missense_variant | Exon 3 of 4 | ENST00000323019.9 | NP_631901.2 | |
MIEF2 | NM_148886.2 | c.200G>A | p.Ser67Asn | missense_variant | Exon 3 of 4 | NP_683684.2 | ||
MIEF2 | NM_001144900.3 | c.167G>A | p.Ser56Asn | missense_variant | Exon 3 of 4 | NP_001138372.1 | ||
MIEF2 | XM_017024190.2 | c.188G>A | p.Ser63Asn | missense_variant | Exon 3 of 4 | XP_016879679.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152252Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000108 AC: 27AN: 250864 AF XY: 0.000111 show subpopulations
GnomAD4 exome AF: 0.000274 AC: 401AN: 1461066Hom.: 0 Cov.: 32 AF XY: 0.000272 AC XY: 198AN XY: 726814 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000177 AC: 27AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74382 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.200G>A (p.S67N) alteration is located in exon 3 (coding exon 3) of the MIEF2 gene. This alteration results from a G to A substitution at nucleotide position 200, causing the serine (S) at amino acid position 67 to be replaced by an asparagine (N). 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