11-122718384-T-C

Variant names:

• chr11-122718384-T-C
• rs10736526
• NM_032873.5:c.162-57835T>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.162-57835T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,136 control chromosomes in the GnomAD database, including 45,884 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 0.77 (45884 hom., cov: 32)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032873.5. 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
	UBASH3B	NM_032873.5	MANE Select	c.162-57835T>C		intron	N/A	NP_116262.2
	UBASH3B	NM_001363365.2		c.53-57835T>C		intron	N/A	NP_001350294.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBASH3B	ENST00000284273.6	TSL:1 MANE Select	c.162-57835T>C		intron	N/A	ENSP00000284273.5
	UBASH3B	ENST00000525711.1	TSL:4	n.487-9130T>C		intron	N/A
	UBASH3B	ENST00000526386.5	TSL:4	n.213+8910T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117828 AN: 152018 Hom.: 45879 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.775 AC: 117877 AN: 152136 Hom.: 45884 Cov.: 32 AF XY: 0.775 AC XY: 57666 AN XY: 74362

African (AFR) AF: 0.706 AC: 29277 AN: 41496

American (AMR) AF: 0.827 AC: 12634 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2795 AN: 3468

East Asian (EAS) AF: 0.917 AC: 4743 AN: 5172

South Asian (SAS) AF: 0.782 AC: 3771 AN: 4822

European-Finnish (FIN) AF: 0.761 AC: 8052 AN: 10584

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53959 AN: 67992

Other (OTH) AF: 0.782 AC: 1651 AN: 2110

Alfa AF: 0.791 Hom.: 123775

Bravo AF: 0.776

Asia WGS AF: 0.785 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.51
PhyloP100		-0.82
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: rs10736526; hg19: chr11-122589092;