chr22-39513842-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_019008.6(MIEF1):c.911G>A(p.Arg304His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00515 in 1,614,054 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0044 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0052 ( 30 hom. )
Consequence
MIEF1
NM_019008.6 missense
NM_019008.6 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 1.17
Genes affected
MIEF1 (HGNC:25979): (mitochondrial elongation factor 1) Enables ADP binding activity; GDP binding activity; and identical protein binding activity. Involved in several processes, including positive regulation of mitochondrial fission; positive regulation of mitochondrial translation; and positive regulation of protein targeting to membrane. Located in mitochondrial matrix and mitochondrial outer membrane. Colocalizes with mitochondrial large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0036183596).
BP6
?
Variant 22-39513842-G-A is Benign according to our data. Variant chr22-39513842-G-A is described in ClinVar as [Benign]. Clinvar id is 787193.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 669 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIEF1 | NM_019008.6 | c.911G>A | p.Arg304His | missense_variant | 6/6 | ENST00000325301.7 | |
MIEF1 | NM_001304564.2 | c.911G>A | p.Arg304His | missense_variant | 6/7 | ||
MIEF1 | NR_130789.2 | n.1312G>A | non_coding_transcript_exon_variant | 6/6 | |||
MIEF1 | NR_130790.2 | n.1462G>A | non_coding_transcript_exon_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIEF1 | ENST00000325301.7 | c.911G>A | p.Arg304His | missense_variant | 6/6 | 1 | NM_019008.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00440 AC: 669AN: 152154Hom.: 2 Cov.: 32
GnomAD3 genomes
?
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32
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GnomAD3 exomes AF: 0.00522 AC: 1313AN: 251312Hom.: 10 AF XY: 0.00547 AC XY: 743AN XY: 135890
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GnomAD4 exome AF: 0.00523 AC: 7641AN: 1461782Hom.: 30 Cov.: 31 AF XY: 0.00511 AC XY: 3715AN XY: 727184
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GnomAD4 genome ? AF: 0.00439 AC: 668AN: 152272Hom.: 2 Cov.: 32 AF XY: 0.00509 AC XY: 379AN XY: 74450
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ESP6500AA
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40
ExAC
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616
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 11, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
P;P;P
Vest4
MVP
MPC
0.52
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at