5-179836446-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003900.5(SQSTM1):c.1176G>A(p.Pro392Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000544 in 1,614,160 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003900.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SQSTM1 | NM_003900.5 | c.1176G>A | p.Pro392Pro | synonymous_variant | Exon 8 of 8 | ENST00000389805.9 | NP_003891.1 | |
SQSTM1 | NM_001142298.2 | c.924G>A | p.Pro308Pro | synonymous_variant | Exon 9 of 9 | NP_001135770.1 | ||
SQSTM1 | NM_001142299.2 | c.924G>A | p.Pro308Pro | synonymous_variant | Exon 9 of 9 | NP_001135771.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000690 AC: 105AN: 152166Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00161 AC: 403AN: 251038Hom.: 4 AF XY: 0.00156 AC XY: 212AN XY: 135718
GnomAD4 exome AF: 0.000529 AC: 773AN: 1461876Hom.: 8 Cov.: 31 AF XY: 0.000514 AC XY: 374AN XY: 727236
GnomAD4 genome AF: 0.000690 AC: 105AN: 152284Hom.: 1 Cov.: 33 AF XY: 0.000792 AC XY: 59AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
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Paget disease of bone 3 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Paget disease of bone 2, early-onset;C5779877:Frontotemporal dementia and/or amyotrophic lateral sclerosis 1 Benign:1
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not provided Benign:1
See Variant Classification Assertion Criteria. -
Paget disease of bone 3;C4225326:Frontotemporal dementia and/or amyotrophic lateral sclerosis 3;C4310693:Neurodegeneration with ataxia, dystonia, and gaze palsy, childhood-onset;C5399975:Myopathy, distal, with rimmed vacuoles Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at