13-52028094-T-TA

Position:

• chr13-52028094-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_021645.6(UTP14C):​c.-486-213dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00778 in 143,996 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0078 (4 hom., cov: 33)
• Consequence: UTP14C NM_021645.6 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.95

Genes affected

UTP14C (HGNC:20321): (UTP14C small subunit processome component) Predicted to be involved in several processes, including meiotic cell cycle; rRNA processing; and spermatogenesis. Located in cytosol and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ALG11 (HGNC:32456): (ALG11 alpha-1,2-mannosyltransferase) This gene encodes a GDP-Man:Man3GlcNAc2-PP-dolichol-alpha1,2-mannosyltransferase which is localized to the cytosolic side of the endoplasmic reticulum (ER) and catalyzes the transfer of the fourth and fifth mannose residue from GDP-mannose (GDP-Man) to Man3GlcNAc2-PP-dolichol and Man4GlcNAc2-PP-dolichol resulting in the production of Man5GlcNAc2-PP-dolichol. Mutations in this gene are associated with congenital disorder of glycosylation type Ip (CDGIP). This gene overlaps but is distinct from the UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast) gene. A pseudogene of the GDP-Man:Man3GlcNAc2-PP-dolichol-alpha1,2-mannosyltransferase has been identified on chromosome 19. [provided by RefSeq, Aug 2010]

ALG11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-52028094-T-TA is Benign according to our data. Variant chr13-52028094-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 1707147.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00778 (1120/143996) while in subpopulation AFR AF= 0.0232 (918/39620). AF 95% confidence interval is 0.0219. There are 4 homozygotes in gnomad4. There are 538 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTP14C	NM_021645.6	c.-486-213dupA		intron_variant		ENST00000521776.2	NP_067677.4
ALG11	NM_001004127.3	c.1208-213dupA		intron_variant		ENST00000521508.2	NP_001004127.2
ALG11	NR_036571.3	n.66-213dupA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTP14C	ENST00000521776.2	c.-486-213dupA		intron_variant		1	NM_021645.6	ENSP00000428619.1
ALG11	ENST00000521508.2	c.1208-213dupA		intron_variant		1	NM_001004127.3	ENSP00000430236.1

Frequencies

GnomAD3 genomes AF: 0.00773 AC: 1113 AN: 143940 Hom.: 4 Cov.: 33

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00480

Gnomad ASJ AF: 0.000890

Gnomad EAS AF: 0.00219

Gnomad SAS AF: 0.000873

Gnomad FIN AF: 0.00481

Gnomad MID AF: 0.00327

Gnomad NFE AF: 0.000872

Gnomad OTH AF: 0.00825

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00778 AC: 1120 AN: 143996 Hom.: 4 Cov.: 33 AF XY: 0.00771 AC XY: 538 AN XY: 69778

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.00480

Gnomad4 ASJ AF: 0.000890

Gnomad4 EAS AF: 0.00220

Gnomad4 SAS AF: 0.000876

Gnomad4 FIN AF: 0.00481

Gnomad4 NFE AF: 0.000872

Gnomad4 OTH AF: 0.00819

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 03, 2020

See Variant Classification Assertion Criteria. -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs142915895; hg19: chr13-52602230;