9-94603132-CT-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_000507.4(FBP1):c.*248del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.51 (20117 hom., cov: 0)
  • Exomes 𝑓: 0.50 (49360 hom.)
• Consequence: FBP1 NM_000507.4 3_prime_UTR
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.192

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]

PCAT7 (HGNC:48824): (prostate cancer associated transcript 7)

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 9-94603132-CT-C is Benign according to our data. Variant chr9-94603132-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 367554.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBP1	NM_000507.4	c.*248del		3_prime_UTR_variant	7/7	ENST00000375326.9
FBP1	NM_001127628.2	c.*248del		3_prime_UTR_variant	8/8
FBP1	XM_006717005.5	c.*248del		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBP1	ENST00000375326.9	c.*248del		3_prime_UTR_variant	7/7	1	NM_000507.4	P1
PCAT7	ENST00000647389.1	n.1642-150del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77796 AN: 151808 Hom.: 20103 Cov.: 0

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.499 AC: 191428 AN: 383548 Hom.: 49360 Cov.: 0 AF XY: 0.496 AC XY: 100053 AN XY: 201860

Gnomad4 AFR exome AF: 0.495

Gnomad4 AMR exome AF: 0.660

Gnomad4 ASJ exome AF: 0.652

Gnomad4 EAS exome AF: 0.387

Gnomad4 SAS exome AF: 0.431

Gnomad4 FIN exome AF: 0.419

Gnomad4 NFE exome AF: 0.510

Gnomad4 OTH exome AF: 0.531

GnomAD4 genome AF: 0.512 AC: 77852 AN: 151926 Hom.: 20117 Cov.: 0 AF XY: 0.509 AC XY: 37776 AN XY: 74236

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.540

Alfa AF: 0.382 Hom.: 982

Bravo AF: 0.530

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Fructose-biphosphatase deficiency Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11351544; hg19: chr9-97365414;