rs148278350
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003900.5(SQSTM1):c.1245G>A(p.Arg415Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000685 in 1,614,198 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003900.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SQSTM1 | NM_003900.5 | c.1245G>A | p.Arg415Arg | synonymous_variant | Exon 8 of 8 | ENST00000389805.9 | NP_003891.1 | |
SQSTM1 | NM_001142298.2 | c.993G>A | p.Arg331Arg | synonymous_variant | Exon 9 of 9 | NP_001135770.1 | ||
SQSTM1 | NM_001142299.2 | c.993G>A | p.Arg331Arg | synonymous_variant | Exon 9 of 9 | NP_001135771.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000769 AC: 117AN: 152190Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00137 AC: 345AN: 251488Hom.: 0 AF XY: 0.00119 AC XY: 162AN XY: 135920
GnomAD4 exome AF: 0.000677 AC: 989AN: 1461890Hom.: 10 Cov.: 31 AF XY: 0.000649 AC XY: 472AN XY: 727248
GnomAD4 genome AF: 0.000762 AC: 116AN: 152308Hom.: 1 Cov.: 33 AF XY: 0.000886 AC XY: 66AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:3
SQSTM1: BP4, BP7, BS1 -
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Paget disease of bone 3 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Paget disease of bone 2, early-onset;C5779877:Frontotemporal dementia and/or amyotrophic lateral sclerosis 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at