rs6010164
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The ENST00000311597.10(MLC1):āc.597A>Gā(p.Ser199=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,612,712 control chromosomes in the GnomAD database, including 13,883 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
ENST00000311597.10 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MLC1 | NM_015166.4 | c.597A>G | p.Ser199= | splice_region_variant, synonymous_variant | 7/12 | ENST00000311597.10 | NP_055981.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLC1 | ENST00000311597.10 | c.597A>G | p.Ser199= | splice_region_variant, synonymous_variant | 7/12 | 1 | NM_015166.4 | ENSP00000310375 | P1 | |
MLC1 | ENST00000395876.6 | c.597A>G | p.Ser199= | splice_region_variant, synonymous_variant | 7/12 | 1 | ENSP00000379216 | P1 | ||
MLC1 | ENST00000442311.1 | c.507A>G | p.Ser169= | splice_region_variant, synonymous_variant | 6/8 | 5 | ENSP00000401385 |
Frequencies
GnomAD3 genomes AF: 0.116 AC: 17630AN: 152046Hom.: 1072 Cov.: 33
GnomAD3 exomes AF: 0.125 AC: 31277AN: 251120Hom.: 2159 AF XY: 0.131 AC XY: 17733AN XY: 135714
GnomAD4 exome AF: 0.129 AC: 188041AN: 1460548Hom.: 12807 Cov.: 32 AF XY: 0.132 AC XY: 95766AN XY: 726692
GnomAD4 genome AF: 0.116 AC: 17647AN: 152164Hom.: 1076 Cov.: 33 AF XY: 0.116 AC XY: 8646AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Megalencephalic leukoencephalopathy with subcortical cysts 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jun 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Megalencephalic leukoencephalopathy with subcortical cysts Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 09, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at