rs796052213
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_StrongPP5
The NM_003900.5(SQSTM1):c.1132A>T(p.Lys378Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. K378K) has been classified as Likely benign.
Frequency
Consequence
NM_003900.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SQSTM1 | NM_003900.5 | c.1132A>T | p.Lys378Ter | stop_gained | 7/8 | ENST00000389805.9 | |
SQSTM1 | NM_001142298.2 | c.880A>T | p.Lys294Ter | stop_gained | 8/9 | ||
SQSTM1 | NM_001142299.2 | c.880A>T | p.Lys294Ter | stop_gained | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SQSTM1 | ENST00000389805.9 | c.1132A>T | p.Lys378Ter | stop_gained | 7/8 | 1 | NM_003900.5 | P1 | |
SQSTM1 | ENST00000360718.5 | c.880A>T | p.Lys294Ter | stop_gained | 6/7 | 1 | |||
SQSTM1 | ENST00000510187.5 | c.950+522A>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461856Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727226
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Paget disease of bone 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at