rs198782
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021242.6(MID1IP1):c.-1815T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.73 ( 21865 hom., 22884 hem., cov: 22)
Exomes 𝑓: 0.74 ( 14 hom. 60 hem. )
Failed GnomAD Quality Control
Consequence
MID1IP1
NM_021242.6 5_prime_UTR
NM_021242.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.784
Genes affected
MID1IP1 (HGNC:20715): (MID1 interacting protein 1) Predicted to enable identical protein binding activity and protein C-terminus binding activity. Predicted to be involved in several processes, including negative regulation of microtubule depolymerization; positive regulation of fatty acid biosynthetic process; and protein polymerization. Predicted to be located in cytoplasm and microtubule cytoskeleton. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MID1IP1 | NM_021242.6 | c.-1815T>C | 5_prime_UTR_variant | 2/3 | ENST00000614558.3 | ||
MID1IP1-AS1 | NR_046706.1 | n.151+870A>G | intron_variant, non_coding_transcript_variant | ||||
MID1IP1 | NM_001098790.2 | c.-369+1376T>C | intron_variant | ||||
MID1IP1 | NM_001098791.2 | c.-265+1376T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MID1IP1 | ENST00000614558.3 | c.-1815T>C | 5_prime_UTR_variant | 2/3 | 5 | NM_021242.6 | P1 | ||
MID1IP1-AS1 | ENST00000436893.1 | n.151+870A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.733 AC: 80330AN: 109621Hom.: 21870 Cov.: 22 AF XY: 0.717 AC XY: 22839AN XY: 31855
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GnomAD4 exome AF: 0.736 AC: 109AN: 148Hom.: 14 Cov.: 0 AF XY: 0.811 AC XY: 60AN XY: 74
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.733 AC: 80362AN: 109675Hom.: 21865 Cov.: 22 AF XY: 0.717 AC XY: 22884AN XY: 31919
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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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