22-23894887-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_002415.2(MIF):c.224C>T(p.Ser75Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,553,982 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002415.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIF | NM_002415.2 | c.224C>T | p.Ser75Phe | missense_variant | 2/3 | ENST00000215754.8 | |
MIF-AS1 | NR_038911.1 | n.1015G>A | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIF | ENST00000215754.8 | c.224C>T | p.Ser75Phe | missense_variant | 2/3 | 1 | NM_002415.2 | P1 | |
MIF-AS1 | ENST00000406213.1 | n.1015G>A | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
MIF | ENST00000465752.1 | n.249C>T | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
MIF | ENST00000498385.1 | n.190C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00128 AC: 195AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00138 AC: 206AN: 149230Hom.: 1 AF XY: 0.00145 AC XY: 119AN XY: 81840
GnomAD4 exome AF: 0.00155 AC: 2176AN: 1401708Hom.: 5 Cov.: 33 AF XY: 0.00159 AC XY: 1101AN XY: 692482
GnomAD4 genome ? AF: 0.00127 AC: 194AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.00129 AC XY: 96AN XY: 74466
ClinVar
Submissions by phenotype
MIF-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at