rs10020551

Variant names:

• chr4-44705798-G-T
• rs10020551
• ENST00000509756.1:c.*1943C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000509756.1(GNPDA2):​c.*1943C>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 0.526 in 151,580 control chromosomes in the GnomAD database, including 22,406 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 0.53 (22406 hom., cov: 31)
  • Exomes 𝑓: 0.38 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GNPDA2 ENST00000509756.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 5 publications found

Genes affected

GNPDA2 (HGNC:21526): (glucosamine-6-phosphate deaminase 2) The protein encoded by this gene is an allosteric enzyme that catalyzes the reversible reaction converting D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium. Variations of this gene have been reported to be associated with influencing body mass index and susceptibility to obesity. A pseudogene of this gene is located on chromosome 9. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Aug 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509756.1. 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
	GNPDA2	NM_138335.3	MANE Select	c.769+1954C>A		intron	N/A	NP_612208.1	Q8TDQ7-1
	GNPDA2	NM_001270880.2		c.667+1954C>A		intron	N/A	NP_001257809.1	Q8TDQ7-5
	GNPDA2	NM_001270881.2		c.559+1954C>A		intron	N/A	NP_001257810.1	Q8TDQ7-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNPDA2	ENST00000509756.1	TSL:1	c.*1943C>A		3_prime_UTR	Exon 6 of 6	ENSP00000424061.1	Q8TDQ7-3
	GNPDA2	ENST00000295448.8	TSL:1 MANE Select	c.769+1954C>A		intron	N/A	ENSP00000295448.3	Q8TDQ7-1
	GNPDA2	ENST00000507917.5	TSL:1	c.667+1954C>A		intron	N/A	ENSP00000425868.1	Q8TDQ7-5

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79736 AN: 151462 Hom.: 22403 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.537

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.375 AC: 3 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.526 AC: 79766 AN: 151580 Hom.: 22406 Cov.: 31 AF XY: 0.525 AC XY: 38911 AN XY: 74084

African (AFR) AF: 0.333 AC: 13798 AN: 41378

American (AMR) AF: 0.495 AC: 7517 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1849 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2053 AN: 5138

South Asian (SAS) AF: 0.490 AC: 2348 AN: 4796

European-Finnish (FIN) AF: 0.681 AC: 7190 AN: 10554

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43100 AN: 67762

Other (OTH) AF: 0.534 AC: 1126 AN: 2108

Alfa AF: 0.562 Hom.: 6222

Bravo AF: 0.511

Asia WGS AF: 0.441 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.81
PhyloP100		-0.72
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10020551;

hg19: chr4-44707815;