Genetic Variant FUS:p.Gly229dup (chr16-31185081-T-TGGC) – ACMG Classification: Benign (-17 pts)

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBS1BS2

The NM_004960.4(FUS):c.684_686dupCGG(p.Gly229dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,607,566 control chromosomes in the GnomAD database, including 12 homozygotes. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G229G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0047 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0011 ( 8 hom. )

Consequence

FUS
NM_004960.4 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 2.17

Publications

2 publications found

Variant links:

Genes affected

FUS (HGNC:4010): (FUS RNA binding protein) This gene encodes a multifunctional protein component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complex. The hnRNP complex is involved in pre-mRNA splicing and the export of fully processed mRNA to the cytoplasm. This protein belongs to the FET family of RNA-binding proteins which have been implicated in cellular processes that include regulation of gene expression, maintenance of genomic integrity and mRNA/microRNA processing. Alternative splicing results in multiple transcript variants. Defects in this gene result in amyotrophic lateral sclerosis type 6. [provided by RefSeq, Sep 2009]

FUS Gene-Disease associations (from GenCC):

amyotrophic lateral sclerosis
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina
amyotrophic lateral sclerosis type 6
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, ClinGen
juvenile amyotrophic lateral sclerosis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
tremor, hereditary essential, 4
Inheritance: AD, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

FUS links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_004960.4

BP6

Variant 16-31185081-T-TGGC is Benign according to our data. Variant chr16-31185081-T-TGGC is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 318986.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00466 (707/151644) while in subpopulation AFR AF = 0.0143 (589/41326). AF 95% confidence interval is 0.0133. There are 4 homozygotes in GnomAd4. There are 346 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 4 AD,AR,Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004960.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
FUS	NM_004960.4	MANE Select	c.684_686dupCGG	p.Gly229dup	disruptive_inframe_insertion	Exon 6 of 15	NP_004951.1
FUS	NM_001170634.1		c.681_683dupCGG	p.Gly228dup	disruptive_inframe_insertion	Exon 6 of 15	NP_001164105.1
FUS	NM_001170937.1		c.672_674dupCGG	p.Gly225dup	disruptive_inframe_insertion	Exon 6 of 15	NP_001164408.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
FUS	ENST00000254108.12	TSL:1 MANE Select	c.684_686dupCGG	p.Gly229dup	disruptive_inframe_insertion	Exon 6 of 15	ENSP00000254108.8
FUS	ENST00000380244.8	TSL:1	c.681_683dupCGG	p.Gly228dup	disruptive_inframe_insertion	Exon 6 of 15	ENSP00000369594.3
FUS	ENST00000566605.5	TSL:1	n.684_686dupCGG		non_coding_transcript_exon	Exon 6 of 14	ENSP00000455073.1

Frequencies

GnomAD3 genomes

AF:

0.00464

AC:

703

AN:

151526

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0142

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00250

Gnomad ASJ

AF:

0.00116

Gnomad EAS

AF:

0.00368

Gnomad SAS

AF:

0.00188

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000575

Gnomad OTH

AF:

0.00336

GnomAD2 exomes

AF:

0.00164

AC:

382

AN:

232882

AF XY:

0.00150

show subpopulations

Gnomad AFR exome

AF:

0.0102

Gnomad AMR exome

AF:

0.00124

Gnomad ASJ exome

AF:

0.000716

Gnomad EAS exome

AF:

0.00317

Gnomad FIN exome

AF:

0.000195

Gnomad NFE exome

AF:

0.000547

Gnomad OTH exome

AF:

0.00241

GnomAD4 exome

AF:

0.00111

AC:

1612

AN:

1455922

Hom.:

Cov.:

AF XY:

0.00104

AC XY:

752

AN XY:

723972

show subpopulations

African (AFR)

AF:

0.0143

AC:

476

AN:

33388

American (AMR)

AF:

0.00136

AC:

AN:

43236

Ashkenazi Jewish (ASJ)

AF:

0.000422

AC:

AN:

26042

East Asian (EAS)

AF:

0.00175

AC:

AN:

39538

South Asian (SAS)

AF:

0.00204

AC:

175

AN:

85976

European-Finnish (FIN)

AF:

0.000209

AC:

AN:

52562

Middle Eastern (MID)

AF:

0.000868

AC:

AN:

5758

European-Non Finnish (NFE)

AF:

0.000559

AC:

620

AN:

1109310

Other (OTH)

AF:

0.00309

AC:

186

AN:

60112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

191

287

382

478

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

144

180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00466

AC:

707

AN:

151644

Hom.:

Cov.:

AF XY:

0.00467

AC XY:

346

AN XY:

74094

show subpopulations

African (AFR)

AF:

0.0143

AC:

589

AN:

41326

American (AMR)

AF:

0.00250

AC:

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.00116

AC:

AN:

3460

East Asian (EAS)

AF:

0.00369

AC:

AN:

5148

South Asian (SAS)

AF:

0.00188

AC:

AN:

4784

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10522

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000575

AC:

AN:

67876

Other (OTH)

AF:

0.00380

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

122

153

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000401

Hom.:

ClinVar

ClinVar submissions as Germline

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

not specified (2)

Amyotrophic lateral sclerosis type 6;C3539195:Tremor, hereditary essential, 4 (1)

Amyotrophic Lateral Sclerosis, Dominant (1)

FUS-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.2

Mutation Taster

=81/19

polymorphism

(source)

Splicing

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

Publications

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16-31185081-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over