rs1060819

chr11-295527-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025092.5(PGGHG):c.*778T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,244 control chromosomes in the GnomAD database, including 39,488 homozygotes. 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 0.72 (39469 hom., cov: 33)
  • Exomes 𝑓: 0.74 (19 hom.)
• Consequence: PGGHG NM_025092.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGGHG	NM_025092.5	c.*778T>C		3_prime_UTR_variant	14/14	ENST00000409548.7
PGGHG	XM_011520384.3	c.*778T>C		3_prime_UTR_variant	14/14
PGGHG	XM_017018355.2	c.*778T>C		3_prime_UTR_variant	14/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGGHG	ENST00000409548.7	c.*778T>C		3_prime_UTR_variant	14/14	1	NM_025092.5	P1
PGGHG	ENST00000409655.5	c.*778T>C		3_prime_UTR_variant	13/13	1
PGGHG	ENST00000474221.5	n.4267T>C		non_coding_transcript_exon_variant	11/11	2
PGGHG	ENST00000476372.1	n.2723T>C		non_coding_transcript_exon_variant	8/8	2

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109188 AN: 152064 Hom.: 39439 Cov.: 33

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.730

GnomAD4 exome AF: 0.742 AC: 46 AN: 62 Hom.: 19 Cov.: 0 AF XY: 0.750 AC XY: 30 AN XY: 40

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.735

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.718 AC: 109267 AN: 152182 Hom.: 39469 Cov.: 33 AF XY: 0.716 AC XY: 53275 AN XY: 74406

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.728

Alfa AF: 0.737 Hom.: 6212

Bravo AF: 0.714

Asia WGS AF: 0.600 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.7
Dann	Benign	0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs1060819; hg19: chr11-295527;