rs4837839
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_198252.3(GSN):c.352-835C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,956 control chromosomes in the GnomAD database, including 12,450 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.36 ( 12432 hom., cov: 31)
Exomes 𝑓: 0.49 ( 18 hom. )
Consequence
GSN
NM_198252.3 intron
NM_198252.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.303
Genes affected
GSN (HGNC:4620): (gelsolin) The protein encoded by this gene binds to the "plus" ends of actin monomers and filaments to prevent monomer exchange. The encoded calcium-regulated protein functions in both assembly and disassembly of actin filaments. Defects in this gene are a cause of familial amyloidosis Finnish type (FAF). Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GSN | NM_198252.3 | c.352-835C>T | intron_variant | ENST00000432226.7 | NP_937895.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GSN | ENST00000432226.7 | c.352-835C>T | intron_variant | 5 | NM_198252.3 | ENSP00000404226 | P1 |
Frequencies
GnomAD3 genomes AF: 0.362 AC: 54959AN: 151702Hom.: 12420 Cov.: 31
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GnomAD4 exome AF: 0.493 AC: 67AN: 136Hom.: 18 Cov.: 0 AF XY: 0.509 AC XY: 57AN XY: 112
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GnomAD4 genome AF: 0.362 AC: 54975AN: 151820Hom.: 12432 Cov.: 31 AF XY: 0.371 AC XY: 27506AN XY: 74168
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at