19-40775513-CCTTGCTCACTCT-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The 19-40775513-CCTTGCTCACTCT-C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,414 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
MIA
NM_006533.4 5_prime_UTR
NM_006533.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.680
Genes affected
MIA (HGNC:7076): (MIA SH3 domain containing) Predicted to enable growth factor activity. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cell-matrix adhesion. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 19-40775513-CCTTGCTCACTCT-C is Benign according to our data. Variant chr19-40775513-CCTTGCTCACTCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 3052511.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MIA | NM_006533.4 | 5_prime_UTR_variant | 1/4 | ENST00000263369.4 | NP_006524.1 | |||
| MIA | NM_001202553.2 | c.-6-14_-6-3del | splice_polypyrimidine_tract_variant, intron_variant | NP_001189482.1 | ||||
| MIA-RAB4B | NR_037775.1 | upstream_gene_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MIA | ENST00000263369.4 | 5_prime_UTR_variant | 1/4 | 1 | NM_006533.4 | ENSP00000263369 | P1 |
Frequencies
GnomAD3 genomes 0.0000197 AC: 3AN: 152120Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461294Hom.: 0 AF XY: 0.0000165 AC XY: 12AN XY: 726938
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GnomAD4 genome 0.0000197 AC: 3AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
MIA-related disorder Benign:1
| Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 29, 2019 | 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
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at