5-179836430-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_003900.5(SQSTM1):c.1166-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,614,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003900.5 splice_region, splice_polypyrimidine_tract, 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SQSTM1 | NM_003900.5 | c.1166-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000389805.9 | |||
SQSTM1 | NM_001142298.2 | c.914-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SQSTM1 | NM_001142299.2 | c.914-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SQSTM1 | ENST00000389805.9 | c.1166-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003900.5 | P1 | |||
SQSTM1 | ENST00000360718.5 | c.914-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
MRNIP | ENST00000522663.5 | c.*1260G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 1 | ||||
SQSTM1 | ENST00000510187.5 | c.951-41C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250708Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135602
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 727232
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
Frontotemporal dementia and/or amyotrophic lateral sclerosis 1;C4085251:Paget disease of bone 2, early-onset Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 03, 2023 | - - |
SQSTM1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 16, 2022 | 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