Variant rs4837839 details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.303

Variant links:

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]

GSN links:

GSN (HGNC:):

GSN links:

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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 linkuse as main transcript	c.352-835C>T		intron_variant		ENST00000432226.7	NP_937895.1	P06396-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSN	ENST00000432226.7 linkuse as main transcript	c.352-835C>T		intron_variant		5	NM_198252.3	ENSP00000404226.2		P06396-2Q5T0I0

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54959

AN:

151702

Hom.:

12420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0845

Gnomad AMI

AF:

0.588

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.436

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.542

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.423

GnomAD4 exome

AF:

0.493

AC:

AN:

136

Hom.:

Cov.:

AF XY:

0.509

AC XY:

AN XY:

112

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.519

Gnomad4 OTH exome

AF:

0.375

GnomAD4 genome

AF:

0.362

AC:

54975

AN:

151820

Hom.:

12432

Cov.:

AF XY:

0.371

AC XY:

27506

AN XY:

74168

show subpopulations

Gnomad4 AFR

AF:

0.0844

Gnomad4 AMR

AF:

0.423

Gnomad4 ASJ

AF:

0.436

Gnomad4 EAS

AF:

0.508

Gnomad4 SAS

AF:

0.590

Gnomad4 FIN

AF:

0.542

Gnomad4 NFE

AF:

0.454

Gnomad4 OTH

AF:

0.426

Alfa

AF:

0.396

Hom.:

1721

Bravo

AF:

0.340

Asia WGS

AF:

0.492

AC:

1712

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.4

DANN

Benign

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over