NM_032873.5:c.162-58343T>C

Variant names:

• chr11-122717876-T-C
• rs11218771
• NM_032873.5:c.162-58343T>C

Variant summary

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

The NM_032873.5(UBASH3B):​c.162-58343T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 150,774 control chromosomes in the GnomAD database, including 12,539 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 0.40 (12539 hom., cov: 28)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 6 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBASH3B	NM_032873.5	c.162-58343T>C		intron_variant	Intron 1 of 13	ENST00000284273.6	NP_116262.2
UBASH3B	NM_001363365.2	c.53-58343T>C		intron_variant	Intron 1 of 13		NP_001350294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBASH3B	ENST00000284273.6	c.162-58343T>C		intron_variant	Intron 1 of 13	1	NM_032873.5	ENSP00000284273.5
UBASH3B	ENST00000525711.1	n.487-9638T>C		intron_variant	Intron 1 of 1	4
UBASH3B	ENST00000526386.5	n.213+8402T>C		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.396 AC: 59715 AN: 150706 Hom.: 12522 Cov.: 28

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.421

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.396 AC: 59747 AN: 150774 Hom.: 12539 Cov.: 28 AF XY: 0.405 AC XY: 29754 AN XY: 73554

African (AFR) AF: 0.289 AC: 11852 AN: 41034

American (AMR) AF: 0.474 AC: 7189 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1850 AN: 3466

East Asian (EAS) AF: 0.724 AC: 3706 AN: 5118

South Asian (SAS) AF: 0.475 AC: 2261 AN: 4764

European-Finnish (FIN) AF: 0.431 AC: 4383 AN: 10160

Middle Eastern (MID) AF: 0.458 AC: 132 AN: 288

European-Non Finnish (NFE) AF: 0.398 AC: 26994 AN: 67786

Other (OTH) AF: 0.420 AC: 877 AN: 2090

Alfa AF: 0.405 Hom.: 38413

Bravo AF: 0.398

Asia WGS AF: 0.529 AC: 1834 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.80
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: rs11218771; hg19: chr11-122588584;