rs1054317

Variant names:

• chr2-128192319-A-C
• rs1054317
• NM_020120.4:c.*2577A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-128192319-A-C
• chr2-128192319-A-G
• chr2-128192319-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020120.4(UGGT1):​c.*2577A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 27)
• Consequence: UGGT1 NM_020120.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 4 publications found

Genes affected

UGGT1 (HGNC:15663): (UDP-glucose glycoprotein glucosyltransferase 1) UDP-glucose:glycoprotein glucosyltransferase (UGT) is a soluble protein of the endoplasmic reticulum (ER) that selectively reglucosylates unfolded glycoproteins, thus providing quality control for protein transport out of the ER.[supplied by OMIM, Oct 2009]

UGGT1 Gene-Disease associations (from GenCC):

• disorder of protein N-glycosylation

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020120.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGGT1	NM_020120.4	MANE Select	c.*2577A>C		3_prime_UTR	Exon 41 of 41	NP_064505.1	Q9NYU2-1
	UGGT1	NR_027671.3		n.7584A>C		non_coding_transcript_exon	Exon 41 of 41

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGGT1	ENST00000259253.11	TSL:1 MANE Select	c.*2577A>C		3_prime_UTR	Exon 41 of 41	ENSP00000259253.6	Q9NYU2-1
	UGGT1	ENST00000933134.1		c.*2577A>C		3_prime_UTR	Exon 41 of 41	ENSP00000603193.1
	UGGT1	ENST00000860373.1		c.*2577A>C		3_prime_UTR	Exon 41 of 41	ENSP00000530432.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 27

Alfa AF: 0.00 Hom.: 3504

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.048
DANN	Benign	0.40
PhyloP100		-2.9
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

Other links and lift over

dbSNP: rs1054317; hg19: chr2-128949893;