X-154521905-T-C

Variant names:

• chrX-154521905-T-C
• rs622
• ENST00000696421.1:c.1458-3457A>G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000696421.1(G6PD):​c.1458-3457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.52 (11682 hom., 15807 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: G6PD ENST00000696421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

G6PD (HGNC:4057): (glucose-6-phosphate dehydrogenase) This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms. G6PD deficiency may cause neonatal jaundice, acute hemolysis, or severe chronic non-spherocytic hemolytic anemia. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

LOC124905229 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905229	XR_007068357.1	n.237-700T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
G6PD	ENST00000696421.1	c.1458-3457A>G		intron_variant	Intron 12 of 12			ENSP00000512616.1
G6PD	ENST00000696420.1	c.1458-3609A>G		intron_variant	Intron 12 of 12			ENSP00000512615.1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 56667 AN: 107935 Hom.: 11687 Cov.: 21 AF XY: 0.513 AC XY: 15789 AN XY: 30751

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.545

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.525 AC: 56668 AN: 107985 Hom.: 11682 Cov.: 21 AF XY: 0.513 AC XY: 15807 AN XY: 30811

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.540

Alfa AF: 0.550 Hom.: 3927

Bravo AF: 0.521

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs622; hg19: chrX-153750119;