chr13-99351854-G-A

Position:

• chr13-99351854-G-A

Variant summary

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

The NM_001144072.2(UBAC2):​c.807+11289G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 440,372 control chromosomes in the GnomAD database, including 5,468 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 0.13 (1578 hom., cov: 32)
  • Exomes 𝑓: 0.15 (3890 hom.)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

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]

FKSG29 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAC2	NM_001144072.2	c.807+11289G>A		intron_variant		ENST00000403766.8	NP_001137544.1
FKSG29	NR_024013.1	n.435G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBAC2	ENST00000403766.8	c.807+11289G>A		intron_variant		2	NM_001144072.2	ENSP00000383911	P1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20190 AN: 152084 Hom.: 1570 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.138

GnomAD3 exomes AF: 0.172 AC: 21828 AN: 126770 Hom.: 2505 AF XY: 0.166 AC XY: 11376 AN XY: 68694

Gnomad AFR exome AF: 0.107

Gnomad AMR exome AF: 0.313

Gnomad ASJ exome AF: 0.0879

Gnomad EAS exome AF: 0.317

Gnomad SAS exome AF: 0.169

Gnomad FIN exome AF: 0.131

Gnomad NFE exome AF: 0.110

Gnomad OTH exome AF: 0.137

GnomAD4 exome AF: 0.146 AC: 42077 AN: 288170 Hom.: 3890 Cov.: 0 AF XY: 0.146 AC XY: 23783 AN XY: 162988

Gnomad4 AFR exome AF: 0.106

Gnomad4 AMR exome AF: 0.310

Gnomad4 ASJ exome AF: 0.0858

Gnomad4 EAS exome AF: 0.320

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.134

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.133 AC: 20212 AN: 152202 Hom.: 1578 Cov.: 32 AF XY: 0.136 AC XY: 10109 AN XY: 74400

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0890

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.140

Alfa AF: 0.120 Hom.: 1845

Bravo AF: 0.140

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.54

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: rs727263; hg19: chr13-100004108;