13-99351854-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001144072.2(UBAC2):​c.807+11289G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000347 in 288,344 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000035 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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>T		intron	N/A	NP_001137544.1
	FKSG29	NR_024013.1		n.435G>T		non_coding_transcript_exon	Exon 1 of 1
	UBAC2	NM_177967.4		c.702+11289G>T		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>T		intron	N/A	ENSP00000383911.3
	UBAC2	ENST00000473194.5	TSL:1	n.574+11289G>T		intron	N/A
	UBAC2	ENST00000480738.1	TSL:1	n.426+11289G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000789 AC: 1 AN: 126770 AF XY: 0.0000146

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000347 AC: 1 AN: 288344 Hom.: 0 Cov.: 0 AF XY: 0.00000613 AC XY: 1 AN XY: 163092

African (AFR) AF: 0.00 AC: 0 AN: 8048

American (AMR) AF: 0.00 AC: 0 AN: 25256

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10106

East Asian (EAS) AF: 0.00 AC: 0 AN: 8908

South Asian (SAS) AF: 0.0000173 AC: 1 AN: 57876

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12488

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2712

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 149520

Other (OTH) AF: 0.00 AC: 0 AN: 13430

GnomAD4 genome Cov.: 32

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	0.74
PhyloP100		0.26

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;