5-141994638-C-T

Variant names:

• chr5-141994638-C-T
• rs409037
• ENST00000513454.5:c.770-2718G>A

Variant summary

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

The ENST00000513454.5(GNPDA1):​c.770-2718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,142 control chromosomes in the GnomAD database, including 58,378 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 0.87 (58378 hom., cov: 30)
• Consequence: GNPDA1 ENST00000513454.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64
• Publications: 8 publications found

Genes affected

GNPDA1 (HGNC:4417): (glucosamine-6-phosphate deaminase 1) Glucosamine-6-phosphate deaminase (EC 3.5.99.6) is an allosteric enzyme that catalyzes the reversible conversion of D-glucosamine-6-phosphate into D-fructose-6-phosphate and ammonium (Arreola et al., 2003 [PubMed 12965206]).[supplied by OMIM, Jan 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNPDA1	ENST00000513454.5	c.770-2718G>A		intron_variant	Intron 6 of 6	5		ENSP00000423494.1

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132957 AN: 152024 Hom.: 58326 Cov.: 30

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.875 AC: 133066 AN: 152142 Hom.: 58378 Cov.: 30 AF XY: 0.875 AC XY: 65091 AN XY: 74362

African (AFR) AF: 0.926 AC: 38450 AN: 41502

American (AMR) AF: 0.907 AC: 13851 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2886 AN: 3470

East Asian (EAS) AF: 0.982 AC: 5081 AN: 5174

South Asian (SAS) AF: 0.906 AC: 4356 AN: 4810

European-Finnish (FIN) AF: 0.801 AC: 8479 AN: 10590

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57212 AN: 68004

Other (OTH) AF: 0.871 AC: 1839 AN: 2112

Alfa AF: 0.854 Hom.: 34715

Bravo AF: 0.885

Asia WGS AF: 0.922 AC: 3205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.44
PhyloP100		-2.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs409037; hg19: chr5-141374203;