9-101421257-A-T

Variant names:

• chr9-101421257-A-T
• rs41308902
• NM_000035.4:c.*552T>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000035.4(ALDOB):​c.*552T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 164,460 control chromosomes in the GnomAD database, including 621 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.079 (541 hom., cov: 32)
  • Exomes 𝑓: 0.096 (80 hom.)
• Consequence: ALDOB NM_000035.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.99

Genes affected

ALDOB (HGNC:417): (aldolase, fructose-bisphosphate B) Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) is a tetrameric glycolytic enzyme that catalyzes the reversible conversion of fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Vertebrates have 3 aldolase isozymes which are distinguished by their electrophoretic and catalytic properties. Differences indicate that aldolases A, B, and C are distinct proteins, the products of a family of related 'housekeeping' genes exhibiting developmentally regulated expression of the different isozymes. The developing embryo produces aldolase A, which is produced in even greater amounts in adult muscle where it can be as much as 5% of total cellular protein. In adult liver, kidney and intestine, aldolase A expression is repressed and aldolase B is produced. In brain and other nervous tissue, aldolase A and C are expressed about equally. There is a high degree of homology between aldolase A and C. Defects in ALDOB cause hereditary fructose intolerance. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 9-101421257-A-T is Benign according to our data. Variant chr9-101421257-A-T is described in ClinVar as [Benign]. Clinvar id is 364298.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDOB	NM_000035.4	c.*552T>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000647789.2	NP_000026.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDOB	ENST00000647789	c.*552T>A		3_prime_UTR_variant	Exon 9 of 9		NM_000035.4	ENSP00000497767.1
ALDOB	ENST00000648064.1	c.*552T>A		downstream_gene_variant				ENSP00000497990.1

Frequencies

GnomAD3 genomes AF: 0.0792 AC: 12056 AN: 152182 Hom.: 541 Cov.: 32

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0765

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0907

GnomAD4 exome AF: 0.0959 AC: 1166 AN: 12160 Hom.: 80 Cov.: 0 AF XY: 0.0941 AC XY: 602 AN XY: 6398

Gnomad4 AFR exome AF: 0.0490

Gnomad4 AMR exome AF: 0.0708

Gnomad4 ASJ exome AF: 0.0865

Gnomad4 EAS exome AF: 0.00291

Gnomad4 SAS exome AF: 0.109

Gnomad4 FIN exome AF: 0.0377

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.0807

GnomAD4 genome AF: 0.0791 AC: 12054 AN: 152300 Hom.: 541 Cov.: 32 AF XY: 0.0783 AC XY: 5830 AN XY: 74474

Gnomad4 AFR AF: 0.0366

Gnomad4 AMR AF: 0.0764

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.0984

Gnomad4 FIN AF: 0.0643

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0898

Alfa AF: 0.0908 Hom.: 87

Bravo AF: 0.0775

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary fructosuria Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.0
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs41308902; hg19: chr9-104183539;