chr9-94558845-T-C

Variant names:

• chr9-94558845-T-C
• rs1048510
• NM_003837.4:c.*93A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.53 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBP2	NM_003837.4	MANE Select	c.*93A>G		3_prime_UTR	Exon 7 of 7	NP_003828.2
	PCAT7	NR_121567.3	MANE Select	n.264-124T>C		intron	N/A
	PCAT7	NR_121566.3		n.264-39T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBP2	ENST00000375337.4	TSL:1 MANE Select	c.*93A>G		3_prime_UTR	Exon 7 of 7	ENSP00000364486.3
	PCAT7	ENST00000644721.3	MANE Select	n.264-124T>C		intron	N/A
	PCAT7	ENST00000452148.4	TSL:2	n.278-124T>C		intron	N/A

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

African (AFR) AF: 0.336 AC: 8210 AN: 24466

American (AMR) AF: 0.588 AC: 20648 AN: 35090

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 14987 AN: 22762

East Asian (EAS) AF: 0.233 AC: 8428 AN: 36116

South Asian (SAS) AF: 0.334 AC: 24368 AN: 72854

European-Finnish (FIN) AF: 0.421 AC: 21294 AN: 50610

Middle Eastern (MID) AF: 0.534 AC: 2643 AN: 4954

European-Non Finnish (NFE) AF: 0.514 AC: 390125 AN: 759362

Other (OTH) AF: 0.495 AC: 23228 AN: 46934

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

African (AFR) AF: 0.334 AC: 13808 AN: 41392

American (AMR) AF: 0.540 AC: 8230 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1208 AN: 5142

South Asian (SAS) AF: 0.313 AC: 1510 AN: 4820

European-Finnish (FIN) AF: 0.413 AC: 4346 AN: 10514

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.518 AC: 35175 AN: 67946

Other (OTH) AF: 0.489 AC: 1031 AN: 2108

Alfa AF: 0.502 Hom.: 54174

Bravo AF: 0.456

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.087
DANN	Benign	0.30
PhyloP100		-3.5
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: rs1048510; hg19: chr9-97321127; COSMIC: COSV64694420;