rs835367

Variant names:

• chr1-59296796-A-G
• rs835367
• ENST00000413489.5:c.-126A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-59296796-A-G
• chr1-59296796-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413489.5(FGGY):​c.-126A>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 ENST00000413489.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 10 publications found

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

ACMG classification

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: ENST00000413489.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	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
	FGGY	NM_001350797.2		c.-376A>G		upstream_gene	N/A	NP_001337726.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGGY	ENST00000413489.5	TSL:3	c.-126A>G		5_prime_UTR	Exon 1 of 5	ENSP00000406607.1
	FGGY	ENST00000582567.1	TSL:4	c.-242A>G		5_prime_UTR	Exon 1 of 3	ENSP00000463260.1
	FGGY	ENST00000371218.8	TSL:1	c.-369A>G		upstream_gene	N/A	ENSP00000360262.4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 63211 AN: 149638 Hom.: 14464 Cov.: 32

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.: 41 Cov.: 0 AF XY: 0.290 AC XY: 106 AN XY: 366

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.500 AC: 11 AN: 22

South Asian (SAS) AF: 0.349 AC: 51 AN: 146

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.215 AC: 62 AN: 288

Other (OTH) AF: 0.400 AC: 4 AN: 10

GnomAD4 genome AF: 0.423 AC: 63290 AN: 149734 Hom.: 14485 Cov.: 32 AF XY: 0.428 AC XY: 31275 AN XY: 73122

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

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
DANN	Benign	0.69
PhyloP100		-0.38
PromoterAI		-0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs835367; hg19: chr1-59762468;