5-179836419-CCTTA-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_003900.5(SQSTM1):c.1166-14_1166-11delTACT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00016 in 1,614,160 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003900.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SQSTM1 | NM_003900.5 | c.1166-14_1166-11delTACT | intron_variant | Intron 7 of 7 | ENST00000389805.9 | NP_003891.1 | ||
SQSTM1 | NM_001142298.2 | c.914-14_914-11delTACT | intron_variant | Intron 8 of 8 | NP_001135770.1 | |||
SQSTM1 | NM_001142299.2 | c.914-14_914-11delTACT | intron_variant | Intron 8 of 8 | NP_001135771.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000196 AC: 49AN: 250388Hom.: 0 AF XY: 0.000185 AC XY: 25AN XY: 135484
GnomAD4 exome AF: 0.000118 AC: 173AN: 1461858Hom.: 2 AF XY: 0.000138 AC XY: 100AN XY: 727224
GnomAD4 genome AF: 0.000565 AC: 86AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74482
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
SQSTM1-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). -
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