chr11-122716864-C-T

Variant names:

• chr11-122716864-C-T
• rs10790522
• NM_032873.5:c.162-59355C>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.162-59355C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,900 control chromosomes in the GnomAD database, including 5,944 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 0.25 (5944 hom., cov: 31)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBASH3B	NM_032873.5	c.162-59355C>T		intron_variant	Intron 1 of 13	ENST00000284273.6	NP_116262.2
UBASH3B	NM_001363365.2	c.53-59355C>T		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.162-59355C>T		intron_variant	Intron 1 of 13	1	NM_032873.5	ENSP00000284273.5
UBASH3B	ENST00000525711.1	n.487-10650C>T		intron_variant	Intron 1 of 1	4
UBASH3B	ENST00000526386.5	n.213+7390C>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38515 AN: 151782 Hom.: 5940 Cov.: 31

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.254 AC: 38507 AN: 151900 Hom.: 5944 Cov.: 31 AF XY: 0.261 AC XY: 19341 AN XY: 74220

African (AFR) AF: 0.0955 AC: 3960 AN: 41460

American (AMR) AF: 0.273 AC: 4161 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3466

East Asian (EAS) AF: 0.625 AC: 3214 AN: 5144

South Asian (SAS) AF: 0.389 AC: 1863 AN: 4786

European-Finnish (FIN) AF: 0.299 AC: 3160 AN: 10558

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19687 AN: 67914

Other (OTH) AF: 0.282 AC: 595 AN: 2110

Alfa AF: 0.285 Hom.: 11462

Bravo AF: 0.245

Asia WGS AF: 0.430 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.56
PhyloP100		-0.72
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: rs10790522; hg19: chr11-122587572;