ENST00000894272.1:c.-176A>G – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000894272.1(FGGY):c.-176A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 150,220 control chromosomes in the GnomAD database, including 14,526 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 0.42 ( 14485 hom., cov: 32)

Exomes 𝑓: 0.27 ( 41 hom. )

Consequence

FGGY
ENST00000894272.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.377

Publications

10 publications found

Variant links:

Genes affected

FGGY (HGNC:25610): (FGGY carbohydrate kinase domain containing) This gene encodes a protein that phosphorylates carbohydrates such as ribulose, ribitol, and L-arabinitol. Genome-wide association studies in some populations have found an association between polymorphisms in this gene and sporadic amyotrophic lateral sclerosis, but studies of other populations have not been able to replicate this association. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

FGGY links:

FGGY-DT (HGNC:55265): (FGGY divergent transcript)

FGGY-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000894272.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
FGGY	NM_001350793.2	c.-461A>G	upstream_gene	N/A	NP_001337722.1
FGGY	NM_001350796.2	c.-247A>G	upstream_gene	N/A	NP_001337725.1	Q96C11-4
FGGY	NM_001350797.2	c.-376A>G	upstream_gene	N/A	NP_001337726.1

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
FGGY	ENST00000894272.1	c.-176A>G	5_prime_UTR	Exon 1 of 17	ENSP00000564331.1
FGGY	ENST00000894273.1	c.-102A>G	5_prime_UTR	Exon 1 of 16	ENSP00000564332.1
FGGY	ENST00000939057.1	c.-455A>G	5_prime_UTR	Exon 1 of 18	ENSP00000609116.1

Frequencies

GnomAD3 genomes

AF:

0.422

AC:

63211

AN:

149638

Hom.:

14464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.574

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.548

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.425

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.384

GnomAD4 exome

AF:

0.272

AC:

132

AN:

486

Hom.:

Cov.:

AF XY:

0.290

AC XY:

106

AN XY:

366

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.349

AC:

AN:

146

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.215

AC:

AN:

288

Other (OTH)

AF:

0.400

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.423

AC:

63290

AN:

149734

Hom.:

14485

Cov.:

AF XY:

0.428

AC XY:

31275

AN XY:

73122

show subpopulations

African (AFR)

AF:

0.574

AC:

23049

AN:

40146

American (AMR)

AF:

0.379

AC:

5757

AN:

15180

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

1158

AN:

3466

East Asian (EAS)

AF:

0.548

AC:

2771

AN:

5060

South Asian (SAS)

AF:

0.453

AC:

2156

AN:

4762

European-Finnish (FIN)

AF:

0.425

AC:

4431

AN:

10432

Middle Eastern (MID)

AF:

0.382

AC:

110

AN:

288

European-Non Finnish (NFE)

AF:

0.336

AC:

22675

AN:

67424

Other (OTH)

AF:

0.382

AC:

795

AN:

2082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1820

3640

5460

7280

9100

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<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:

0.371

Hom.:

7420

Bravo

AF:

0.426

Asia WGS

AF:

0.351

AC:

991

AN:

2814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

6.0

(source)

DANN

Benign

0.69

PhyloP100

-0.38

PromoterAI

-0.025

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over