chr5-179836424-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003900.5(SQSTM1):c.1166-12C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,882 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 (★).
Frequency
Consequence
NM_003900.5 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SQSTM1 | NM_003900.5 | c.1166-12C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000389805.9 | |||
SQSTM1 | NM_001142298.2 | c.914-12C>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
SQSTM1 | NM_001142299.2 | c.914-12C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SQSTM1 | ENST00000389805.9 | c.1166-12C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003900.5 | P1 | |||
SQSTM1 | ENST00000360718.5 | c.914-12C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
MRNIP | ENST00000522663.5 | c.*1266G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 1 | ||||
SQSTM1 | ENST00000510187.5 | c.951-47C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727242
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Paget disease of bone 2, early-onset;C5779877:Frontotemporal dementia and/or amyotrophic lateral sclerosis 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 24, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.