rs534271877
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_012216.4(MID2):c.1428G>A(p.Ala476=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000408 in 1,208,044 control chromosomes in the GnomAD database, including 3 homozygotes. There are 292 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., 11 hem., cov: 23)
Exomes 𝑓: 0.00043 ( 3 hom. 281 hem. )
Consequence
MID2
NM_012216.4 synonymous
NM_012216.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.23
Genes affected
MID2 (HGNC:7096): (midline 2) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to microtubular structures in the cytoplasm. Alternate splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant X-107917732-G-A is Benign according to our data. Variant chrX-107917732-G-A is described in ClinVar as [Benign]. Clinvar id is 435868.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=1.23 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd4 at 11 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID2 | NM_012216.4 | c.1428G>A | p.Ala476= | synonymous_variant | 7/10 | ENST00000262843.11 | |
LOC101928335 | NR_110395.1 | n.326+15298C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID2 | ENST00000262843.11 | c.1428G>A | p.Ala476= | synonymous_variant | 7/10 | 1 | NM_012216.4 | ||
ENST00000663626.2 | n.556+15298C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000178 AC: 20AN: 112465Hom.: 1 Cov.: 23 AF XY: 0.000318 AC XY: 11AN XY: 34619
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GnomAD3 exomes AF: 0.000760 AC: 139AN: 182856Hom.: 1 AF XY: 0.00122 AC XY: 82AN XY: 67420
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GnomAD4 exome AF: 0.000434 AC: 475AN: 1095525Hom.: 3 Cov.: 29 AF XY: 0.000779 AC XY: 281AN XY: 360949
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GnomAD4 genome ? AF: 0.000160 AC: 18AN: 112519Hom.: 0 Cov.: 23 AF XY: 0.000317 AC XY: 11AN XY: 34683
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 27, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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