rs11207520

chr1-59809423-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_947426.3(LOC105378758):n.309+804A>C variant causes a intron, non coding transcript 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: LOC105378758 XR_947426.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

LOC105378758 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378758	XR_947426.3	n.309+804A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGGY	ENST00000634606.1	c.*1862T>G		3_prime_UTR_variant, NMD_transcript_variant	17/17	5

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

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

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.247

Alfa AF: 0.284 Hom.: 12904

Bravo AF: 0.288

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.43
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11207520; hg19: chr1-60275095;