NM_001144072.2:c.10A>G

Variant names:

• chr13-99200918-A-G
• rs1003294870
• NM_001144072.2:c.10A>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001144072.2(UBAC2):​c.10A>G​(p.Ser4Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S4R) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBAC2 NM_001144072.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.41
• Publications: 0 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]

UBAC2-AS1 (HGNC:42502): (UBAC2 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17892721).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	NM_001144072.2	MANE Select	c.10A>G	p.Ser4Gly	missense	Exon 1 of 9	NP_001137544.1	Q8NBM4-1
	UBAC2	NM_177967.4		c.-494A>G		5_prime_UTR	Exon 1 of 7	NP_808882.1	Q8NBM4-2
	UBAC2	NR_026644.2		n.65A>G		non_coding_transcript_exon	Exon 1 of 9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAC2	ENST00000403766.8	TSL:2 MANE Select	c.10A>G	p.Ser4Gly	missense	Exon 1 of 9	ENSP00000383911.3	Q8NBM4-1
	UBAC2	ENST00000961156.1		c.10A>G	p.Ser4Gly	missense	Exon 1 of 10	ENSP00000631215.1
	UBAC2	ENST00000858721.1		c.10A>G	p.Ser4Gly	missense	Exon 1 of 10	ENSP00000528780.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1154668 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 552828

African (AFR) AF: 0.00 AC: 0 AN: 24646

American (AMR) AF: 0.00 AC: 0 AN: 15928

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15114

East Asian (EAS) AF: 0.00 AC: 0 AN: 29802

South Asian (SAS) AF: 0.00 AC: 0 AN: 28718

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38320

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4626

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 951482

Other (OTH) AF: 0.00 AC: 0 AN: 46032

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.054	T
Eigen	Benign	-0.18
Eigen_PC	Benign	-0.046
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.78	T
M_CAP	Uncertain	0.15	D
MetaRNN	Benign	0.18	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.9	M
PhyloP100		4.4
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-2.2	N
REVEL	Benign	0.076
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.038	D
Polyphen		0.0020	B
Vest4		0.42
MutPred		0.14		Loss of glycosylation at S4 (P = 0.0062)
MVP		0.50
MPC		1.0
ClinPred		0.95	D
GERP RS		3.5
PromoterAI		0.057	Neutral
Varity_R		0.21
gMVP		0.27
Mutation Taster		=54/46	polymorphism

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: rs1003294870; hg19: chr13-99853172;