Variant X-154532439-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP6_ModerateBP7

The NM_001360016.2(G6PD):c.1311T>C(p.Tyr437=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.83 ( 27364 hom., 27660 hem., cov: 24)

Exomes 𝑓: 0.87 ( 280377 hom. 311397 hem. )

Failed GnomAD Quality Control

Consequence

G6PD
NM_001360016.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.64

Variant links:

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]

G6PD links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

BP6

Variant X-154532439-A-G is Benign according to our data. Variant chrX-154532439-A-G is described in ClinVar as [Benign]. Clinvar id is 470162.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.64 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
G6PD	NM_001360016.2 linkuse as main transcript	c.1311T>C	p.Tyr437=	synonymous_variant	11/13	ENST00000393562.10	NP_001346945.1
G6PD	NM_000402.4 linkuse as main transcript	c.1401T>C	p.Tyr467=	synonymous_variant	11/13		NP_000393.4
G6PD	NM_001042351.3 linkuse as main transcript	c.1311T>C	p.Tyr437=	synonymous_variant	11/13		NP_001035810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
G6PD	ENST00000393562.10 linkuse as main transcript	c.1311T>C	p.Tyr437=	synonymous_variant	11/13	1	NM_001360016.2	ENSP00000377192	P4	P11413-1

Frequencies

GnomAD3 genomes

AF:

0.832

AC:

92541

AN:

111243

Hom.:

27365

Cov.:

AF XY:

0.826

AC XY:

27610

AN XY:

33441

show subpopulations

Gnomad AFR

AF:

0.745

Gnomad AMI

AF:

0.883

Gnomad AMR

AF:

0.821

Gnomad ASJ

AF:

0.802

Gnomad EAS

AF:

0.883

Gnomad SAS

AF:

0.575

Gnomad FIN

AF:

0.927

Gnomad MID

AF:

0.820

Gnomad NFE

AF:

0.884

Gnomad OTH

AF:

0.830

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.867

AC:

951577

AN:

1097713

Hom.:

280377

Cov.:

AF XY:

0.857

AC XY:

311397

AN XY:

363219

show subpopulations

Gnomad4 AFR exome

AF:

0.743

Gnomad4 AMR exome

AF:

0.806

Gnomad4 ASJ exome

AF:

0.801

Gnomad4 EAS exome

AF:

0.933

Gnomad4 SAS exome

AF:

0.617

Gnomad4 FIN exome

AF:

0.920

Gnomad4 NFE exome

AF:

0.888

Gnomad4 OTH exome

AF:

0.841

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.832

AC:

92585

AN:

111295

Hom.:

27364

Cov.:

AF XY:

0.826

AC XY:

27660

AN XY:

33503

show subpopulations

Gnomad4 AFR

AF:

0.745

Gnomad4 AMR

AF:

0.821

Gnomad4 ASJ

AF:

0.802

Gnomad4 EAS

AF:

0.883

Gnomad4 SAS

AF:

0.578

Gnomad4 FIN

AF:

0.927

Gnomad4 NFE

AF:

0.884

Gnomad4 OTH

AF:

0.833

Alfa

AF:

0.869

Hom.:

66387

Bravo

AF:

0.829

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Anemia, nonspherocytic hemolytic, due to G6PD deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

-0.020

CADD

Benign

0.0040

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over