13-99384164-A-G

Variant names:

• chr13-99384164-A-G
• rs9557207
• NM_001144072.2:c.928-1064A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144072.2(UBAC2):​c.928-1064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,176 control chromosomes in the GnomAD database, including 2,408 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 0.17 (2408 hom., cov: 33)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144072.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	NM_001144072.2	MANE Select	c.928-1064A>G		intron	N/A	NP_001137544.1
	UBAC2	NM_177967.4		c.823-1064A>G		intron	N/A	NP_808882.1
	UBAC2	NR_026644.2		n.1611-1064A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.928-1064A>G		intron	N/A	ENSP00000383911.3
	UBAC2	ENST00000473194.5	TSL:1	n.695-1064A>G		intron	N/A
	UBAC2	ENST00000480738.1	TSL:1	n.547-1064A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25772 AN: 152058 Hom.: 2406 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.169 AC: 25771 AN: 152176 Hom.: 2408 Cov.: 33 AF XY: 0.164 AC XY: 12237 AN XY: 74390

African (AFR) AF: 0.111 AC: 4602 AN: 41518

American (AMR) AF: 0.170 AC: 2601 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 907 AN: 3470

East Asian (EAS) AF: 0.0560 AC: 290 AN: 5182

South Asian (SAS) AF: 0.122 AC: 588 AN: 4818

European-Finnish (FIN) AF: 0.111 AC: 1175 AN: 10586

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14822 AN: 67996

Other (OTH) AF: 0.203 AC: 429 AN: 2112

Alfa AF: 0.206 Hom.: 4834

Bravo AF: 0.174

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.13
DANN	Benign	0.81
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs9557207; hg19: chr13-100036418;