NM_001370062.2:c.41G>A

Variant names:

• chr9-34017108-C-T
• rs1785506
• NM_001370062.2:c.41G>A

Variant summary

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

The NM_001370062.2(UBAP2):​c.41G>A​(p.Arg14Gln) variant causes a missense change. The variant allele was found at a frequency of 0.619 in 1,610,116 control chromosomes in the GnomAD database, including 311,513 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 0.60 (27877 hom., cov: 31)
  • Exomes 𝑓: 0.62 (283636 hom.)
• Consequence: UBAP2 NM_001370062.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.25
• Publications: 40 publications found

Genes affected

UBAP2 (HGNC:14185): (ubiquitin associated protein 2) The protein encoded by this gene contains a UBA (ubiquitin associated) domain, which is characteristic of proteins that function in the ubiquitination pathway. This gene may show increased expression in the adrenal gland and lymphatic tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=1.2650975E-6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370062.2. 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
	UBAP2	NM_001370062.2	MANE Select	c.41G>A	p.Arg14Gln	missense	Exon 2 of 29	NP_001356991.2
	UBAP2	NM_001370059.2		c.41G>A	p.Arg14Gln	missense	Exon 2 of 29	NP_001356988.2
	UBAP2	NM_018449.4		c.41G>A	p.Arg14Gln	missense	Exon 2 of 29	NP_060919.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBAP2	ENST00000379238.7	TSL:5 MANE Select	c.41G>A	p.Arg14Gln	missense	Exon 2 of 29	ENSP00000368540.2
	UBAP2	ENST00000682239.1		c.41G>A	p.Arg14Gln	missense	Exon 2 of 29	ENSP00000507293.1
	UBAP2	ENST00000684158.1		c.41G>A	p.Arg14Gln	missense	Exon 3 of 30	ENSP00000508372.1

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91337 AN: 151730 Hom.: 27866 Cov.: 31

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.635

GnomAD2 exomes AF: 0.635 AC: 158071 AN: 248838 AF XY: 0.627

Gnomad AFR exome AF: 0.521

Gnomad AMR exome AF: 0.771

Gnomad ASJ exome AF: 0.701

Gnomad EAS exome AF: 0.836

Gnomad FIN exome AF: 0.552

Gnomad NFE exome AF: 0.620

Gnomad OTH exome AF: 0.629

GnomAD4 exome AF: 0.621 AC: 905225 AN: 1458274 Hom.: 283636 Cov.: 45 AF XY: 0.617 AC XY: 447884 AN XY: 725406

African (AFR) AF: 0.519 AC: 17305 AN: 33332

American (AMR) AF: 0.762 AC: 33602 AN: 44108

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 18310 AN: 26078

East Asian (EAS) AF: 0.775 AC: 30694 AN: 39592

South Asian (SAS) AF: 0.519 AC: 44303 AN: 85398

European-Finnish (FIN) AF: 0.555 AC: 29573 AN: 53330

Middle Eastern (MID) AF: 0.646 AC: 3720 AN: 5758

European-Non Finnish (NFE) AF: 0.621 AC: 689901 AN: 1110448

Other (OTH) AF: 0.628 AC: 37817 AN: 60230

GnomAD4 genome AF: 0.602 AC: 91380 AN: 151842 Hom.: 27877 Cov.: 31 AF XY: 0.602 AC XY: 44645 AN XY: 74204

African (AFR) AF: 0.527 AC: 21817 AN: 41378

American (AMR) AF: 0.696 AC: 10606 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2484 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4217 AN: 5176

South Asian (SAS) AF: 0.523 AC: 2518 AN: 4810

European-Finnish (FIN) AF: 0.568 AC: 5968 AN: 10506

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41787 AN: 67962

Other (OTH) AF: 0.634 AC: 1337 AN: 2108

Alfa AF: 0.622 Hom.: 74398

Bravo AF: 0.618

TwinsUK AF: 0.625 AC: 2318

ALSPAC AF: 0.632 AC: 2434

ESP6500AA AF: 0.533 AC: 2347

ESP6500EA AF: 0.617 AC: 5309

ExAC AF: 0.626 AC: 76003

Asia WGS AF: 0.648 AC: 2248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.48	T
BayesDel_noAF	Benign	-0.33
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.12	T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Benign	0.68	T
MetaRNN	Benign	0.0000013	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		6.2
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-1.3	N
REVEL	Benign	0.14
Sift	Benign	0.20	T
Sift4G	Benign	0.082	T
Polyphen		0.90	P
Vest4		0.22
MPC		0.12
ClinPred		0.011	T
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.20
gMVP		0.30
Mutation Taster		=282/18	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: rs1785506; hg19: chr9-34017106; COSMIC: COSV62545718;