rs1048510

Positions:

• chr9-94558845-T-C

Variant summary

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

The NM_003837.4(FBP2):​c.*93A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,204,990 control chromosomes in the GnomAD database, including 145,393 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 0.45 (16154 hom., cov: 31)
  • Exomes 𝑓: 0.49 (129239 hom.)
• Consequence: FBP2 NM_003837.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52

Genes affected

FBP2 (HGNC:3607): (fructose-bisphosphatase 2) This gene encodes a gluconeogenesis regulatory enzyme which catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate and inorganic phosphate. [provided by RefSeq, Jul 2008]

PCAT7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBP2	NM_003837.4	c.*93A>G		3_prime_UTR_variant	7/7	ENST00000375337.4	NP_003828.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBP2	ENST00000375337	c.*93A>G		3_prime_UTR_variant	7/7	1	NM_003837.4	ENSP00000364486.3
PCAT7	ENST00000452148.3	n.258-124T>C		intron_variant		2
PCAT7	ENST00000644721.1	n.264-124T>C		intron_variant
PCAT7	ENST00000647389.1	n.258-124T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68363 AN: 151724 Hom.: 16137 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.496

GnomAD4 exome AF: 0.488 AC: 513931 AN: 1053148 Hom.: 129239 Cov.: 13 AF XY: 0.484 AC XY: 260052 AN XY: 537426

Gnomad4 AFR exome AF: 0.336

Gnomad4 AMR exome AF: 0.588

Gnomad4 ASJ exome AF: 0.658

Gnomad4 EAS exome AF: 0.233

Gnomad4 SAS exome AF: 0.334

Gnomad4 FIN exome AF: 0.421

Gnomad4 NFE exome AF: 0.514

Gnomad4 OTH exome AF: 0.495

GnomAD4 genome AF: 0.451 AC: 68410 AN: 151842 Hom.: 16154 Cov.: 31 AF XY: 0.445 AC XY: 33044 AN XY: 74196

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.489

Alfa AF: 0.514 Hom.: 35279

Bravo AF: 0.456

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.087
DANN	Benign	0.30

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: rs1048510; hg19: chr9-97321127; COSMIC: COSV64694420;