5-141994638-C-T

Position:

• chr5-141994638-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.141994638C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNPDA1	ENST00000513454.5	c.770-2718G>A		intron_variant		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

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.871

Alfa AF: 0.854 Hom.: 31629

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs409037; hg19: chr5-141374203;