5-179836413-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BS1BS2_Supporting
The NM_003900.5(SQSTM1):c.1166-23T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003900.5 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SQSTM1 | NM_003900.5 | c.1166-23T>C | intron_variant | Intron 7 of 7 | ENST00000389805.9 | NP_003891.1 | ||
SQSTM1 | NM_001142298.2 | c.914-23T>C | intron_variant | Intron 8 of 8 | NP_001135770.1 | |||
SQSTM1 | NM_001142299.2 | c.914-23T>C | intron_variant | Intron 8 of 8 | NP_001135771.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000799 AC: 20AN: 250416Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135490
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727230
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74356
ClinVar
Submissions by phenotype
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at