20-36545063-CGCTGGGTGA-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_006097.5(MYL9):c.184+2_184+10delTGAGCTGGG variant causes a splice donor, splice region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,478 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006097.5 splice_donor, splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYL9 | NM_006097.5 | c.184+2_184+10delTGAGCTGGG | splice_donor_variant, splice_region_variant, intron_variant | Intron 2 of 3 | ENST00000279022.7 | NP_006088.2 | ||
MYL9 | NM_181526.3 | c.184+2_184+10delTGAGCTGGG | splice_donor_variant, splice_region_variant, intron_variant | Intron 2 of 2 | NP_852667.1 | |||
DLGAP4-AS1 | NR_109939.1 | n.467+26369_467+26377delTCACCCAGC | intron_variant | Intron 2 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYL9 | ENST00000279022.7 | c.180_184+4delGCTGGGTGA | p.Leu61AsnfsTer110 | frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant | Exon 2 of 4 | 1 | NM_006097.5 | ENSP00000279022.2 | ||
MYL9 | ENST00000346786.2 | c.180_184+4delGCTGGGTGA | p.Leu61IlefsTer56 | frameshift_variant, splice_donor_variant, splice_region_variant, intron_variant | Exon 2 of 3 | 1 | ENSP00000217313.2 | |||
DLGAP4-AS1 | ENST00000439595.5 | n.467+26369_467+26377delTCACCCAGC | intron_variant | Intron 2 of 4 | 1 | |||||
DLGAP4-AS1 | ENST00000425233.6 | n.580-17148_580-17140delTCACCCAGC | intron_variant | Intron 2 of 6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250924Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135632
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461478Hom.: 0 AF XY: 0.00000825 AC XY: 6AN XY: 727066
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Megacystis-microcolon-intestinal hypoperistalsis syndrome 4 Pathogenic:1
- -
Visceral myopathy 1 Uncertain:1
This intronic variant, NM_006097.4:c.184+2_184+10del, was identified in trans with a heterozygous deletion of exon 4 in an individual with a clinical diagnosis of MMIH syndrome: bilateral hydronephrosis, megacystis, congenital bilateral mydriasis, lack of urinary bladder peristalsis, and intestinal pseudo-obstruction. This intronic variant alters the highly conserved splice donor site for exon 2 of this transcript and is predicted by five splice site prediction tools queried to abolish canonical splice donor activity. This variant is expected to result in altered function of the MYL9 gene product as a result of aberrant splicing. This variant has been observed at a frequency of less than 0.01% (2/245706 alleles) across the entire Broad data set (individuals without severe childhood onset disease). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at