9-94576714-C-T

Variant names:

• chr9-94576714-C-T
• rs600130
• NM_003837.4:c.427-5112G>A

Variant summary

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

The NM_003837.4(FBP2):​c.427-5112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,350 control chromosomes in the GnomAD database, including 65,052 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 0.92 (65041 hom., cov: 33)
  • Exomes 𝑓: 0.88 (11 hom.)
• Consequence: FBP2 NM_003837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 6 publications found

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:48824): (prostate cancer associated transcript 7)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003837.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBP2	NM_003837.4	MANE Select	c.427-5112G>A		intron	N/A	NP_003828.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBP2	ENST00000375337.4	TSL:1 MANE Select	c.427-5112G>A		intron	N/A	ENSP00000364486.3	O00757
	PCAT7	ENST00000647389.1		n.600C>T		non_coding_transcript_exon	Exon 4 of 9

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140577 AN: 152206 Hom.: 64986 Cov.: 33

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.932

GnomAD4 exome AF: 0.885 AC: 23 AN: 26 Hom.: 11 Cov.: 0 AF XY: 0.850 AC XY: 17 AN XY: 20

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

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) AF: 1.00 AC: 20 AN: 20

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.924 AC: 140689 AN: 152324 Hom.: 65041 Cov.: 33 AF XY: 0.922 AC XY: 68637 AN XY: 74474

African (AFR) AF: 0.950 AC: 39477 AN: 41568

American (AMR) AF: 0.895 AC: 13693 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.943 AC: 3275 AN: 3472

East Asian (EAS) AF: 0.847 AC: 4394 AN: 5190

South Asian (SAS) AF: 0.850 AC: 4101 AN: 4824

European-Finnish (FIN) AF: 0.935 AC: 9929 AN: 10618

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62730 AN: 68032

Other (OTH) AF: 0.930 AC: 1968 AN: 2116

Alfa AF: 0.916 Hom.: 33215

Bravo AF: 0.920

Asia WGS AF: 0.859 AC: 2984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.3
DANN	Benign	0.62
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs600130; hg19: chr9-97338996;