rs1060819

Variant names:

• chr11-295527-T-C
• rs1060819
• NM_025092.5:c.*778T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-295527-T-C
• chr11-295527-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025092.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGGHG	NM_025092.5	MANE Select	c.*778T>C		3_prime_UTR	Exon 14 of 14	NP_079368.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGGHG	ENST00000409548.7	TSL:1 MANE Select	c.*778T>C		3_prime_UTR	Exon 14 of 14	ENSP00000387185.2
	PGGHG	ENST00000409655.5	TSL:1	c.*778T>C		3_prime_UTR	Exon 13 of 13	ENSP00000386297.1
	PGGHG	ENST00000474221.5	TSL:2	n.4267T>C		non_coding_transcript_exon	Exon 11 of 11

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 12 AN: 16

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.735 AC: 25 AN: 34

Other (OTH) AF: 1.00 AC: 6 AN: 6

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

African (AFR) AF: 0.701 AC: 29113 AN: 41518

American (AMR) AF: 0.694 AC: 10605 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2821 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2426 AN: 5174

South Asian (SAS) AF: 0.689 AC: 3330 AN: 4832

European-Finnish (FIN) AF: 0.729 AC: 7722 AN: 10594

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50674 AN: 67994

Other (OTH) AF: 0.728 AC: 1536 AN: 2110

Alfa AF: 0.736 Hom.: 12124

Bravo AF: 0.714

Asia WGS AF: 0.600 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.76
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1060819; hg19: chr11-295527;