chr9-101442332-C-T

Position:

• chr9-101442332-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746862.2(LOC105376184):​n.190C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,026 control chromosomes in the GnomAD database, including 33,602 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 0.66 (33602 hom., cov: 32)
• Consequence: LOC105376184 XR_001746862.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

Genes affected

LOC105376184 (HGNC:):

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376184	XR_001746862.2	n.190C>T		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDOB	ENST00000648423.1	c.-133G>A		5_prime_UTR_variant	1/4
ALDOB	ENST00000648758.1	c.-79G>A		5_prime_UTR_variant	1/9			P1
ALDOB	ENST00000648064.1	c.-11+7196G>A		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100646 AN: 151908 Hom.: 33579 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.680

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.662 AC: 100712 AN: 152026 Hom.: 33602 Cov.: 32 AF XY: 0.659 AC XY: 48950 AN XY: 74306

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.685

Alfa AF: 0.697 Hom.: 68857

Bravo AF: 0.655

Asia WGS AF: 0.620 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs573816; hg19: chr9-104204614;