rs1927726

chr13-99260629-G-Achr13-99260629-G-C

Variant summary

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

The NM_001144072.2(UBAC2):c.389+16005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,174 control chromosomes in the GnomAD database, including 52,508 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 0.83 (52508 hom., cov: 32)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

UBAC2 (HGNC:20486): (UBA domain containing 2) Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

GPR18 (HGNC:4472): (G protein-coupled receptor 18) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in positive regulation of Rho protein signal transduction and positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway. Predicted to act upstream of or within T cell differentiation; negative regulation of leukocyte chemotaxis; and negative regulation of tumor necrosis factor production. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC124903198 (HGNC:):

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 = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBAC2	NM_001144072.2	c.389+16005G>A		intron_variant		ENST00000403766.8
LOC124903198	XR_007063846.1	n.83-381C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBAC2	ENST00000403766.8	c.389+16005G>A		intron_variant		2	NM_001144072.2	P1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125813 AN: 152056 Hom.: 52471 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.827 AC: 125896 AN: 152174 Hom.: 52508 Cov.: 32 AF XY: 0.826 AC XY: 61459 AN XY: 74412

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.831

Alfa AF: 0.843 Hom.: 8368

Bravo AF: 0.815

Asia WGS AF: 0.737 AC: 2566 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	0.36
Dann	Benign	0.58

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: rs1927726; hg19: chr13-99912883;