rs61736600
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_020533.3(MCOLN1):āc.966A>Cā(p.Arg322=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0709 in 1,613,996 control chromosomes in the GnomAD database, including 4,600 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. R322R) has been classified as Likely benign.
Frequency
Consequence
NM_020533.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCOLN1 | NM_020533.3 | c.966A>C | p.Arg322= | synonymous_variant | 8/14 | ENST00000264079.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCOLN1 | ENST00000264079.11 | c.966A>C | p.Arg322= | synonymous_variant | 8/14 | 1 | NM_020533.3 | P1 | |
MCOLN1 | ENST00000394321.9 | n.1281A>C | non_coding_transcript_exon_variant | 7/13 | 2 | ||||
MCOLN1 | ENST00000595860.5 | n.32A>C | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0591 AC: 8988AN: 152052Hom.: 318 Cov.: 33
GnomAD3 exomes AF: 0.0561 AC: 14099AN: 251278Hom.: 519 AF XY: 0.0570 AC XY: 7746AN XY: 135824
GnomAD4 exome AF: 0.0722 AC: 105513AN: 1461826Hom.: 4280 Cov.: 34 AF XY: 0.0710 AC XY: 51627AN XY: 727218
GnomAD4 genome ? AF: 0.0591 AC: 8990AN: 152170Hom.: 320 Cov.: 33 AF XY: 0.0563 AC XY: 4187AN XY: 74382
ClinVar
Submissions by phenotype
Mucolipidosis type IV Benign:5
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 13, 2021 | - - |
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 12, 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. - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 25, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:2
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 26, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at