5-179833238-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003900.5(SQSTM1):c.961C>T(p.Arg321Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00184 in 1,580,682 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003900.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SQSTM1 | NM_003900.5 | c.961C>T | p.Arg321Cys | missense_variant | Exon 6 of 8 | ENST00000389805.9 | NP_003891.1 | |
SQSTM1 | NM_001142298.2 | c.709C>T | p.Arg237Cys | missense_variant | Exon 7 of 9 | NP_001135770.1 | ||
SQSTM1 | NM_001142299.2 | c.709C>T | p.Arg237Cys | missense_variant | Exon 7 of 9 | NP_001135771.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SQSTM1 | ENST00000389805.9 | c.961C>T | p.Arg321Cys | missense_variant | Exon 6 of 8 | 1 | NM_003900.5 | ENSP00000374455.4 | ||
SQSTM1 | ENST00000360718.5 | c.709C>T | p.Arg237Cys | missense_variant | Exon 5 of 7 | 1 | ENSP00000353944.5 | |||
SQSTM1 | ENST00000510187.5 | c.950+11C>T | intron_variant | Intron 6 of 6 | 5 | ENSP00000424477.1 | ||||
SQSTM1 | ENST00000466342.1 | n.660C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00859 AC: 1307AN: 152160Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.00279 AC: 525AN: 188286Hom.: 11 AF XY: 0.00232 AC XY: 239AN XY: 102954
GnomAD4 exome AF: 0.00111 AC: 1592AN: 1428404Hom.: 15 Cov.: 36 AF XY: 0.00100 AC XY: 710AN XY: 708468
GnomAD4 genome AF: 0.00860 AC: 1309AN: 152278Hom.: 14 Cov.: 33 AF XY: 0.00862 AC XY: 642AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:2
This variant is associated with the following publications: (PMID: 32036052, 31859009, 31434890, 24899140, 22084127) -
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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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
SQSTM1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Paget disease of bone 2, early-onset;C5779877:Frontotemporal dementia and/or amyotrophic lateral sclerosis 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at