NM_032873.5:c.882T>G

Variant names:

• chr11-122789210-T-G
• rs955051
• NM_032873.5:c.882T>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_032873.5(UBASH3B):​c.882T>G​(p.Gly294Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,613,960 control chromosomes in the GnomAD database, including 20,100 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 0.12 (1356 hom., cov: 32)
  • Exomes 𝑓: 0.15 (18744 hom.)
• Consequence: UBASH3B NM_032873.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 12 publications found

Genes affected

UBASH3B (HGNC:29884): (ubiquitin associated and SH3 domain containing B) This gene encodes a protein that contains a ubiquitin associated domain at the N-terminus, an SH3 domain, and a C-terminal domain with similarities to the catalytic motif of phosphoglycerate mutase. The encoded protein was found to inhibit endocytosis of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor. [provided by RefSeq, Jul 2008]

ENSG00000285909 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP7: Synonymous conserved (PhyloP=1.17 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBASH3B	NM_032873.5	c.882T>G	p.Gly294Gly	synonymous_variant	Exon 6 of 14	ENST00000284273.6	NP_116262.2
UBASH3B	NM_001363365.2	c.777T>G	p.Gly259Gly	synonymous_variant	Exon 6 of 14		NP_001350294.1
UBASH3B	XM_005271712.4	c.966T>G	p.Gly322Gly	synonymous_variant	Exon 6 of 14		XP_005271769.1
UBASH3B	XM_011543041.3	c.825T>G	p.Gly275Gly	synonymous_variant	Exon 6 of 14		XP_011541343.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBASH3B	ENST00000284273.6	c.882T>G	p.Gly294Gly	synonymous_variant	Exon 6 of 14	1	NM_032873.5	ENSP00000284273.5

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18118 AN: 151986 Hom.: 1361 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.143

GnomAD2 exomes AF: 0.135 AC: 33998 AN: 251328 AF XY: 0.144

Gnomad AFR exome AF: 0.0437

Gnomad AMR exome AF: 0.0762

Gnomad ASJ exome AF: 0.264

Gnomad EAS exome AF: 0.0406

Gnomad FIN exome AF: 0.0724

Gnomad NFE exome AF: 0.167

Gnomad OTH exome AF: 0.163

GnomAD4 exome AF: 0.154 AC: 225019 AN: 1461856 Hom.: 18744 Cov.: 33 AF XY: 0.156 AC XY: 113623 AN XY: 727228

African (AFR) AF: 0.0452 AC: 1514 AN: 33480

American (AMR) AF: 0.0823 AC: 3680 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 6985 AN: 26136

East Asian (EAS) AF: 0.0332 AC: 1317 AN: 39700

South Asian (SAS) AF: 0.183 AC: 15808 AN: 86258

European-Finnish (FIN) AF: 0.0745 AC: 3979 AN: 53418

Middle Eastern (MID) AF: 0.225 AC: 1297 AN: 5766

European-Non Finnish (NFE) AF: 0.163 AC: 181027 AN: 1111980

Other (OTH) AF: 0.156 AC: 9412 AN: 60394

GnomAD4 genome AF: 0.119 AC: 18110 AN: 152104 Hom.: 1356 Cov.: 32 AF XY: 0.115 AC XY: 8561 AN XY: 74340

African (AFR) AF: 0.0473 AC: 1964 AN: 41488

American (AMR) AF: 0.104 AC: 1592 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3472

East Asian (EAS) AF: 0.0370 AC: 191 AN: 5166

South Asian (SAS) AF: 0.181 AC: 874 AN: 4820

European-Finnish (FIN) AF: 0.0668 AC: 708 AN: 10602

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11412 AN: 67972

Other (OTH) AF: 0.142 AC: 299 AN: 2110

Alfa AF: 0.154 Hom.: 6606

Bravo AF: 0.116

Asia WGS AF: 0.103 AC: 360 AN: 3478

EpiCase AF: 0.182

EpiControl AF: 0.180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		1.2
Mutation Taster		=98/2	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: rs955051; hg19: chr11-122659918; COSMIC: COSV52492037;