Variant 1-10417384-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002631.4(PGD):c.984C>T(p.Tyr328Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000676 in 1,609,468 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00052 ( 2 hom. )

Consequence

PGD
NM_002631.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0940

Variant links:

Genes affected

PGD (HGNC:8891): (phosphogluconate dehydrogenase) 6-phosphogluconate dehydrogenase is the second dehydrogenase in the pentose phosphate shunt. Deficiency of this enzyme is generally asymptomatic, and the inheritance of this disorder is autosomal dominant. Hemolysis results from combined deficiency of 6-phosphogluconate dehydrogenase and 6-phosphogluconolactonase suggesting a synergism of the two enzymopathies. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2015]

PGD links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 1-10417384-C-T is Benign according to our data. Variant chr1-10417384-C-T is described in ClinVar as [Benign]. Clinvar id is 734224.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.094 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGD	NM_002631.4 link	c.984C>T	p.Tyr328Tyr	synonymous_variant	10/13	ENST00000270776.13	NP_002622.2	P52209-1
PGD	NM_001304452.2 link	c.945C>T	p.Tyr315Tyr	synonymous_variant	10/13		NP_001291381.1	P52209-2
PGD	NM_001304451.2 link	c.918C>T	p.Tyr306Tyr	synonymous_variant	9/12		NP_001291380.1	P52209B4E2U0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PGD	ENST00000270776.13 link	c.984C>T	p.Tyr328Tyr	synonymous_variant	10/13	1	NM_002631.4	ENSP00000270776.8	P52209-1
PGD	ENST00000483936.5 link	c.549C>T	p.Tyr183Tyr	synonymous_variant	6/6	5		ENSP00000466156.1	K7ELN9
PGD	ENST00000498356.1 link	n.241C>T		non_coding_transcript_exon_variant	3/6	3

Frequencies

GnomAD3 genomes

AF:

0.00214

AC:

325

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00538

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00414

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000265

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00141

AC:

348

AN:

247298

Hom.:

AF XY:

0.00129

AC XY:

173

AN XY:

133698

show subpopulations

Gnomad AFR exome

AF:

0.00673

Gnomad AMR exome

AF:

0.00130

Gnomad ASJ exome

AF:

0.000411

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000402

Gnomad FIN exome

AF:

0.00467

Gnomad NFE exome

AF:

0.000634

Gnomad OTH exome

AF:

0.00133

GnomAD4 exome

AF:

0.000524

AC:

763

AN:

1457172

Hom.:

Cov.:

AF XY:

0.000488

AC XY:

354

AN XY:

724842

show subpopulations

Gnomad4 AFR exome

AF:

0.00513

Gnomad4 AMR exome

AF:

0.00111

Gnomad4 ASJ exome

AF:

0.000233

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000339

Gnomad4 FIN exome

AF:

0.00484

Gnomad4 NFE exome

AF:

0.000188

Gnomad4 OTH exome

AF:

0.000682

GnomAD4 genome

AF:

0.00213

AC:

325

AN:

152296

Hom.:

Cov.:

AF XY:

0.00231

AC XY:

172

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00537

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.00414

Gnomad4 NFE

AF:

0.000265

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.000450

Hom.:

Bravo

AF:

0.00193

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

4.7

DANN

Benign

0.39

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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