5-179821121-G-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.185G>T(p.Gly62Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000945 in 1,375,064 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G62G) has been classified as Likely benign.
Frequency
Consequence
NM_003900.5 missense
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.185G>T | p.Gly62Val | missense_variant | 1/8 | ENST00000389805.9 | |
SQSTM1 | NM_001142298.2 | c.-47-1837G>T | intron_variant | ||||
SQSTM1 | NM_001142299.2 | c.-47-1837G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SQSTM1 | ENST00000389805.9 | c.185G>T | p.Gly62Val | missense_variant | 1/8 | 1 | NM_003900.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152038Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000518 AC: 10AN: 19306Hom.: 0 AF XY: 0.000733 AC XY: 9AN XY: 12280
GnomAD4 exome AF: 0.0000965 AC: 118AN: 1222918Hom.: 1 Cov.: 31 AF XY: 0.000143 AC XY: 85AN XY: 593636
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152146Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74380
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 | Dec 22, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 24, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at