chrX-38805211-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021242.6(MID1IP1):āc.265A>Gā(p.Ser89Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000457 in 1,094,954 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_021242.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID1IP1 | NM_021242.6 | c.265A>G | p.Ser89Gly | missense_variant | 3/3 | ENST00000614558.3 | |
MID1IP1 | NM_001098790.2 | c.265A>G | p.Ser89Gly | missense_variant | 3/3 | ||
MID1IP1 | NM_001098791.2 | c.265A>G | p.Ser89Gly | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID1IP1 | ENST00000614558.3 | c.265A>G | p.Ser89Gly | missense_variant | 3/3 | 5 | NM_021242.6 | P1 | |
MID1IP1 | ENST00000336949.7 | c.265A>G | p.Ser89Gly | missense_variant | 2/2 | 1 | P1 | ||
MID1IP1 | ENST00000378474.3 | c.265A>G | p.Ser89Gly | missense_variant | 3/3 | 1 | P1 | ||
MID1IP1 | ENST00000457894.5 | c.265A>G | p.Ser89Gly | missense_variant | 2/2 | 3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.0000168 AC: 3AN: 178505Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 64263
GnomAD4 exome AF: 0.00000457 AC: 5AN: 1094954Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 360662
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.265A>G (p.S89G) alteration is located in exon 2 (coding exon 1) of the MID1IP1 gene. This alteration results from a A to G substitution at nucleotide position 265, causing the serine (S) at amino acid position 89 to be replaced by a glycine (G). 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