chr22-50064163-TAGC-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_015166.4(MLC1):c.927_929delGCT(p.Leu310del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000525 in 1,600,600 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015166.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MLC1 | NM_015166.4 | c.927_929delGCT | p.Leu310del | disruptive_inframe_deletion | Exon 11 of 12 | ENST00000311597.10 | NP_055981.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLC1 | ENST00000311597.10 | c.927_929delGCT | p.Leu310del | disruptive_inframe_deletion | Exon 11 of 12 | 1 | NM_015166.4 | ENSP00000310375.6 | ||
MLC1 | ENST00000395876.6 | c.927_929delGCT | p.Leu310del | disruptive_inframe_deletion | Exon 11 of 12 | 1 | ENSP00000379216.2 | |||
MLC1 | ENST00000483836.1 | n.284_286delGCT | non_coding_transcript_exon_variant | Exon 4 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151904Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000545 AC: 79AN: 1448696Hom.: 0 AF XY: 0.0000596 AC XY: 43AN XY: 720970
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151904Hom.: 0 Cov.: 34 AF XY: 0.0000404 AC XY: 3AN XY: 74192
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.927_929del, results in the deletion of 1 amino acid(s) of the MLC1 protein (p.Leu310del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with MLC1-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
MLC1-related disorder Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at