rs10750218

Variant names:

• chr11-122685870-A-G
• rs10750218
• NM_032873.5:c.161+29660A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-122685870-A-G
• chr11-122685870-A-T

Variant summary

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

The NM_032873.5(UBASH3B):​c.161+29660A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,006 control chromosomes in the GnomAD database, including 39,461 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 0.69 (39461 hom., cov: 32)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.819 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.161+29660A>G		intron	N/A	NP_116262.2
	UBASH3B	NM_001363365.2		c.52+29660A>G		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.161+29660A>G		intron	N/A	ENSP00000284273.5
	UBASH3B	ENST00000525711.1	TSL:4	n.486+29660A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104721 AN: 151888 Hom.: 39458 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.689 AC: 104751 AN: 152006 Hom.: 39461 Cov.: 32 AF XY: 0.693 AC XY: 51467 AN XY: 74286

African (AFR) AF: 0.354 AC: 14683 AN: 41430

American (AMR) AF: 0.832 AC: 12706 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2853 AN: 3472

East Asian (EAS) AF: 0.787 AC: 4051 AN: 5148

South Asian (SAS) AF: 0.734 AC: 3533 AN: 4814

European-Finnish (FIN) AF: 0.808 AC: 8536 AN: 10566

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.822 AC: 55850 AN: 67984

Other (OTH) AF: 0.728 AC: 1536 AN: 2110

Alfa AF: 0.784 Hom.: 66221

Bravo AF: 0.677

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.94
DANN	Benign	0.35
PhyloP100		-1.6
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: rs10750218; hg19: chr11-122556578;