Variant chr6-83166527-AAAAT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015599.3(PGM3):c.*2703_*2706del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0156 in 684,910 control chromosomes in the GnomAD database, including 370 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.029 ( 150 hom., cov: 32)

Exomes 𝑓: 0.012 ( 220 hom. )

Consequence

PGM3
NM_015599.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.347

Variant links:

Genes affected

PGM3 (HGNC:8907): (phosphoglucomutase 3) This gene encodes a member of the phosphohexose mutase family. The encoded protein mediates both glycogen formation and utilization by catalyzing the interconversion of glucose-1-phosphate and glucose-6-phosphate. A non-synonymous single nucleotide polymorphism in this gene may play a role in resistance to diabetic nephropathy and neuropathy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

PGM3 links:

DOP1A (HGNC:21194): (DOP1 leucine zipper like protein A) Predicted to be involved in Golgi to endosome transport and endoplasmic reticulum organization. Predicted to be located in Golgi membrane. Predicted to be active in endosome and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

DOP1A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 6-83166527-AAAAT-A is Benign according to our data. Variant chr6-83166527-AAAAT-A is described in ClinVar as [Benign]. Clinvar id is 1175579.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGM3	NM_015599.3 linkuse as main transcript	c.2703_2706del		3_prime_UTR_variant	13/13	ENST00000513973.6	NP_056414.1
DOP1A	NM_015018.4 linkuse as main transcript	c.7093-1329_7093-1326del		intron_variant		ENST00000349129.7	NP_055833.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGM3	ENST00000513973.6 linkuse as main transcript	c.2703_2706del		3_prime_UTR_variant	13/13	1	NM_015599.3	ENSP00000424874	P1	O95394-1
DOP1A	ENST00000349129.7 linkuse as main transcript	c.7093-1329_7093-1326del		intron_variant		1	NM_015018.4	ENSP00000195654	P4

Frequencies

GnomAD3 genomes

AF:

0.0285

AC:

4333

AN:

152164

Hom.:

146

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0775

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0266

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0827

Gnomad SAS

AF:

0.0363

Gnomad FIN

AF:

0.000565

Gnomad MID

AF:

0.0255

Gnomad NFE

AF:

0.000735

Gnomad OTH

AF:

0.0225

GnomAD4 exome

AF:

0.0119

AC:

6353

AN:

532628

Hom.:

220

AF XY:

0.0123

AC XY:

3512

AN XY:

286470

show subpopulations

Gnomad4 AFR exome

AF:

0.0814

Gnomad4 AMR exome

AF:

0.0139

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0662

Gnomad4 SAS exome

AF:

0.0318

Gnomad4 FIN exome

AF:

0.000430

Gnomad4 NFE exome

AF:

0.000968

Gnomad4 OTH exome

AF:

0.0147

GnomAD4 genome

AF:

0.0285

AC:

4347

AN:

152282

Hom.:

150

Cov.:

AF XY:

0.0289

AC XY:

2152

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0776

Gnomad4 AMR

AF:

0.0265

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0827

Gnomad4 SAS

AF:

0.0363

Gnomad4 FIN

AF:

0.000565

Gnomad4 NFE

AF:

0.000735

Gnomad4 OTH

AF:

0.0232

Alfa

AF:

0.0160

Hom.:

Bravo

AF:

0.0316

Asia WGS

AF:

0.0630

AC:

218

AN:

3478

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

GeneDx

Jul 30, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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