Variant 11-290466-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The ENST00000409655.5(PGGHG):c.-216C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00782 in 1,549,980 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0082 ( 67 hom. )

Consequence

PGGHG
ENST00000409655.5 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.275

Variant links:

Genes affected

PGGHG (HGNC:26210): (protein-glucosylgalactosylhydroxylysine glucosidase) Enables protein-glucosylgalactosylhydroxylysine glucosidase activity. Involved in carbohydrate metabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

PGGHG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 11-290466-C-T is Benign according to our data. Variant chr11-290466-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3341584.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGGHG	NM_025092.5 linkuse as main transcript	c.336C>T	p.His112His	synonymous_variant	3/14	ENST00000409548.7	NP_079368.3	Q32M88-1A0A024R1Z9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGGHG	ENST00000409548.7 linkuse as main transcript	c.336C>T	p.His112His	synonymous_variant	3/14	1	NM_025092.5	ENSP00000387185.2		Q32M88-1

Frequencies

GnomAD3 genomes

AF:

0.00468

AC:

712

AN:

152228

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00157

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00537

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00833

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00461

AC:

708

AN:

153430

Hom.:

AF XY:

0.00461

AC XY:

377

AN XY:

81754

show subpopulations

Gnomad AFR exome

AF:

0.00116

Gnomad AMR exome

AF:

0.00187

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00404

Gnomad FIN exome

AF:

0.00154

Gnomad NFE exome

AF:

0.00890

Gnomad OTH exome

AF:

0.00254

GnomAD4 exome

AF:

0.00816

AC:

11410

AN:

1397634

Hom.:

Cov.:

AF XY:

0.00788

AC XY:

5430

AN XY:

689358

show subpopulations

Gnomad4 AFR exome

AF:

0.00127

Gnomad4 AMR exome

AF:

0.00202

Gnomad4 ASJ exome

AF:

0.0000795

Gnomad4 EAS exome

AF:

0.0000840

Gnomad4 SAS exome

AF:

0.00406

Gnomad4 FIN exome

AF:

0.00225

Gnomad4 NFE exome

AF:

0.00963

Gnomad4 OTH exome

AF:

0.00794

GnomAD4 genome

AF:

0.00467

AC:

712

AN:

152346

Hom.:

Cov.:

AF XY:

0.00422

AC XY:

314

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00156

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00538

Gnomad4 FIN

AF:

0.00122

Gnomad4 NFE

AF:

0.00833

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00696

Hom.:

Bravo

AF:

0.00498

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

PGGHG: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

0.60

DANN

Benign

0.94

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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