13-99385979-A-G

Position:

• chr13-99385979-A-G

Variant summary

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

The NM_001144072.2(UBAC2):​c.*644A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,588 control chromosomes in the GnomAD database, including 30,415 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 0.63 (30287 hom., cov: 33)
  • Exomes 𝑓: 0.71 (128 hom.)
• Consequence: UBAC2 NM_001144072.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

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]

UBAC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAC2	NM_001144072.2	c.*644A>G		3_prime_UTR_variant	9/9	ENST00000403766.8	NP_001137544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBAC2	ENST00000403766.8	c.*644A>G		3_prime_UTR_variant	9/9	2	NM_001144072.2	ENSP00000383911.3
UBAC2	ENST00000376440.6	c.*644A>G		3_prime_UTR_variant	7/7	2		ENSP00000365623.2
UBAC2	ENST00000460562.5	n.1895A>G		non_coding_transcript_exon_variant	6/6	2
UBAC2	ENST00000494576.5	n.1400A>G		non_coding_transcript_exon_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95526 AN: 151960 Hom.: 30269 Cov.: 33

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.604

GnomAD4 exome AF: 0.714 AC: 364 AN: 510 Hom.: 128 Cov.: 0 AF XY: 0.712 AC XY: 225 AN XY: 316

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.857

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.800

Gnomad4 FIN exome AF: 0.730

Gnomad4 NFE exome AF: 0.670

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.629 AC: 95582 AN: 152078 Hom.: 30287 Cov.: 33 AF XY: 0.632 AC XY: 47001 AN XY: 74344

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.603

Alfa AF: 0.642 Hom.: 63916

Bravo AF: 0.612

Asia WGS AF: 0.613 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.0
DANN	Benign	0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1058083; hg19: chr13-100038233;