chr9-94603438-T-G

Variant names:

• chr9-94603438-T-G
• rs1769257
• NM_000507.4:c.960A>C

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_000507.4(FBP1):​c.960A>C​(p.Gly320Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G320G) has been classified as Benign.

• Frequency: Genomes: not found (cov: 29)
• Consequence: FBP1 NM_000507.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 25 publications found

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

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP7: Synonymous conserved (PhyloP=-0.565 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000507.4. 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
	FBP1	NM_000507.4	MANE Select	c.960A>C	p.Gly320Gly	synonymous	Exon 7 of 7	NP_000498.2
	FBP1	NM_001127628.2		c.960A>C	p.Gly320Gly	synonymous	Exon 8 of 8	NP_001121100.1	P09467

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBP1	ENST00000375326.9	TSL:1 MANE Select	c.960A>C	p.Gly320Gly	synonymous	Exon 7 of 7	ENSP00000364475.5	P09467
	FBP1	ENST00000884868.1		c.1128A>C	p.Gly376Gly	synonymous	Exon 8 of 8	ENSP00000554927.1
	FBP1	ENST00000945615.1		c.1128A>C	p.Gly376Gly	synonymous	Exon 7 of 7	ENSP00000615674.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 54

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 32121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		-0.56

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: rs1769257; hg19: chr9-97365720;