rs28369760

Variant names:

• chr9-94605616-TAAGA-T
• rs28369760
• NM_000507.4:c.706-44_706-41delTCTT

Your query was ambiguous. Multiple possible variants found:

• chr9-94605616-TAAGA-T
• chr9-94605616-TAAGA-TAAGAAAGA

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_000507.4(FBP1):​c.706-44_706-41delTCTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.081 in 1,607,244 control chromosomes in the GnomAD database, including 6,310 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.085 (655 hom., cov: 31)
  • Exomes 𝑓: 0.081 (5655 hom.)
• Consequence: FBP1 NM_000507.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.150
• Publications: 4 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]

FBP1 Gene-Disease associations (from GenCC):

• fructose-1,6-bisphosphatase deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia, Genomics England PanelApp, Orphanet

ACMG classification

Our verdict: Benign. The variant received -16 ACMG points.

• BP6: Variant 9-94605616-TAAGA-T is Benign according to our data. Variant chr9-94605616-TAAGA-T is described in ClinVar as Benign. ClinVar VariationId is 256325.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBP1	NM_000507.4	c.706-44_706-41delTCTT		intron_variant	Intron 5 of 6	ENST00000375326.9	NP_000498.2
FBP1	NM_001127628.2	c.706-44_706-41delTCTT		intron_variant	Intron 6 of 7		NP_001121100.1
FBP1	XM_006717005.5	c.460-44_460-41delTCTT		intron_variant	Intron 5 of 6		XP_006717068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBP1	ENST00000375326.9	c.706-44_706-41delTCTT		intron_variant	Intron 5 of 6	1	NM_000507.4	ENSP00000364475.5
FBP1	ENST00000415431.5	c.706-44_706-41delTCTT		intron_variant	Intron 6 of 7	2		ENSP00000408025.1
FBP1	ENST00000648117.1	c.511-44_511-41delTCTT		intron_variant	Intron 4 of 5			ENSP00000498145.1
FBP1	ENST00000682520.1	n.*143-44_*143-41delTCTT		intron_variant	Intron 5 of 6			ENSP00000507547.1

Frequencies

GnomAD3 genomes AF: 0.0851 AC: 12932 AN: 151994 Hom.: 651 Cov.: 31

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0868

GnomAD2 exomes AF: 0.102 AC: 24551 AN: 241162 AF XY: 0.100

Gnomad AFR exome AF: 0.0810

Gnomad AMR exome AF: 0.183

Gnomad ASJ exome AF: 0.104

Gnomad EAS exome AF: 0.222

Gnomad FIN exome AF: 0.0444

Gnomad NFE exome AF: 0.0649

Gnomad OTH exome AF: 0.0876

GnomAD4 exome AF: 0.0806 AC: 117276 AN: 1455132 Hom.: 5655 AF XY: 0.0816 AC XY: 59041 AN XY: 723726

African (AFR) AF: 0.0807 AC: 2694 AN: 33366

American (AMR) AF: 0.178 AC: 7865 AN: 44128

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 2733 AN: 25980

East Asian (EAS) AF: 0.175 AC: 6924 AN: 39560

South Asian (SAS) AF: 0.126 AC: 10740 AN: 85456

European-Finnish (FIN) AF: 0.0442 AC: 2346 AN: 53130

Middle Eastern (MID) AF: 0.0970 AC: 558 AN: 5752

European-Non Finnish (NFE) AF: 0.0701 AC: 77620 AN: 1107646

Other (OTH) AF: 0.0964 AC: 5796 AN: 60114

GnomAD4 genome AF: 0.0851 AC: 12952 AN: 152112 Hom.: 655 Cov.: 31 AF XY: 0.0858 AC XY: 6376 AN XY: 74342

African (AFR) AF: 0.0819 AC: 3401 AN: 41508

American (AMR) AF: 0.138 AC: 2105 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1120 AN: 5158

South Asian (SAS) AF: 0.134 AC: 647 AN: 4814

European-Finnish (FIN) AF: 0.0411 AC: 435 AN: 10592

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0686 AC: 4666 AN: 67988

Other (OTH) AF: 0.0911 AC: 192 AN: 2108

Alfa AF: 0.0784 Hom.: 97

Bravo AF: 0.0942

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Jun 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.15
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: rs28369760; hg19: chr9-97367898;