rs4129220

chr9-94627816-G-A

Variant summary

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

The NM_000507.4(FBP1):c.171-7325C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,040 control chromosomes in the GnomAD database, including 10,186 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 0.36 (10186 hom., cov: 32)
• Consequence: FBP1 NM_000507.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

FBP1 (HGNC:3606): (fructose-bisphosphatase 1) Fructose-1,6-bisphosphatase 1, a gluconeogenesis regulatory enzyme, catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate and inorganic phosphate. Fructose-1,6-diphosphatase deficiency is associated with hypoglycemia and metabolic acidosis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBP1	NM_000507.4	c.171-7325C>T		intron_variant		ENST00000375326.9
FBP1	NM_001127628.2	c.171-7325C>T		intron_variant
FBP1	XM_006717005.5	c.-76-7325C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBP1	ENST00000375326.9	c.171-7325C>T		intron_variant		1	NM_000507.4	P1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55126 AN: 151922 Hom.: 10180 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.386

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.363 AC: 55160 AN: 152040 Hom.: 10186 Cov.: 32 AF XY: 0.359 AC XY: 26677 AN XY: 74316

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.382

Alfa AF: 0.378 Hom.: 16856

Bravo AF: 0.371

Asia WGS AF: 0.220 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.81
Dann	Benign	0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129220; hg19: chr9-97390098;