NM_001144072.2:c.807+11289G>A

Variant names:

• chr13-99351854-G-A
• rs727263
• NM_001144072.2:c.807+11289G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 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]

FKSG29 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.807+11289G>A		intron	N/A	NP_001137544.1
	FKSG29	NR_024013.1		n.435G>A		non_coding_transcript_exon	Exon 1 of 1
	UBAC2	NM_177967.4		c.702+11289G>A		intron	N/A	NP_808882.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.807+11289G>A		intron	N/A	ENSP00000383911.3
	UBAC2	ENST00000473194.5	TSL:1	n.574+11289G>A		intron	N/A
	UBAC2	ENST00000480738.1	TSL:1	n.426+11289G>A		intron	N/A

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

GnomAD2 exomes AF: 0.172 AC: 21828 AN: 126770 AF XY: 0.166

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 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

African (AFR) AF: 0.106 AC: 850 AN: 8046

American (AMR) AF: 0.310 AC: 7819 AN: 25206

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 866 AN: 10098

East Asian (EAS) AF: 0.320 AC: 2850 AN: 8906

South Asian (SAS) AF: 0.167 AC: 9662 AN: 57858

European-Finnish (FIN) AF: 0.134 AC: 1675 AN: 12478

Middle Eastern (MID) AF: 0.0885 AC: 240 AN: 2712

European-Non Finnish (NFE) AF: 0.110 AC: 16436 AN: 149440

Other (OTH) AF: 0.125 AC: 1679 AN: 13426

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

African (AFR) AF: 0.113 AC: 4700 AN: 41530

American (AMR) AF: 0.209 AC: 3194 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1664 AN: 5168

South Asian (SAS) AF: 0.164 AC: 790 AN: 4826

European-Finnish (FIN) AF: 0.134 AC: 1421 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7792 AN: 68018

Other (OTH) AF: 0.140 AC: 294 AN: 2102

Alfa AF: 0.122 Hom.: 2525

Bravo AF: 0.140

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.54
PhyloP100		0.26
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: rs727263; hg19: chr13-100004108; COSMIC: COSV107449485; COSMIC: COSV107449485;