chr1-59809423-T-G

Variant names:

• chr1-59809423-T-G
• rs11207520
• ENST00000634606.1:n.*1862T>G

Variant summary

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

The ENST00000634606.1(FGGY):​n.*1862T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,038 control chromosomes in the GnomAD database, including 6,801 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 0.29 (6801 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: FGGY ENST00000634606.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 2 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]

LOC105378758 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634606.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGGY	ENST00000634606.1	TSL:5	n.*1862T>G		non_coding_transcript_exon	Exon 17 of 17	ENSP00000489030.1
	FGGY	ENST00000634606.1	TSL:5	n.*1862T>G		3_prime_UTR	Exon 17 of 17	ENSP00000489030.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44539 AN: 151920 Hom.: 6790 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.249

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.293 AC: 44577 AN: 152038 Hom.: 6801 Cov.: 32 AF XY: 0.291 AC XY: 21666 AN XY: 74326

African (AFR) AF: 0.321 AC: 13306 AN: 41448

American (AMR) AF: 0.280 AC: 4285 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3466

East Asian (EAS) AF: 0.139 AC: 721 AN: 5176

South Asian (SAS) AF: 0.195 AC: 941 AN: 4824

European-Finnish (FIN) AF: 0.335 AC: 3532 AN: 10548

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20503 AN: 67972

Other (OTH) AF: 0.247 AC: 522 AN: 2112

Alfa AF: 0.288 Hom.: 20259

Bravo AF: 0.288

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.52
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs11207520; hg19: chr1-60275095;