NM_000381.4:c.2000C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000381.4(MID1):c.2000C>T(p.Pro667Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00142 in 1,205,410 control chromosomes in the GnomAD database, including 14 homozygotes. There are 525 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P667P) has been classified as Likely benign.
Frequency
Consequence
NM_000381.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MID1 | NM_000381.4 | c.2000C>T | p.Pro667Leu | missense_variant | Exon 10 of 10 | ENST00000317552.9 | NP_000372.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00266 AC: 297AN: 111632Hom.: 2 Cov.: 23 AF XY: 0.00331 AC XY: 112AN XY: 33816
GnomAD3 exomes AF: 0.00556 AC: 1006AN: 180978Hom.: 9 AF XY: 0.00425 AC XY: 281AN XY: 66126
GnomAD4 exome AF: 0.00129 AC: 1409AN: 1093728Hom.: 12 Cov.: 29 AF XY: 0.00115 AC XY: 413AN XY: 359500
GnomAD4 genome AF: 0.00266 AC: 297AN: 111682Hom.: 2 Cov.: 23 AF XY: 0.00331 AC XY: 112AN XY: 33876
ClinVar
Submissions by phenotype
X-linked Opitz G/BBB syndrome Uncertain:1Benign:1
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not specified Benign:2
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not provided Benign:2
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MID1: BS2 -
Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at