11-122763559-T-C

Variant names:

• chr11-122763559-T-C
• rs12804711
• NM_032873.5:c.162-12660T>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.162-12660T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,116 control chromosomes in the GnomAD database, including 1,980 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 0.15 (1980 hom., cov: 32)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 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.162-12660T>C		intron	N/A	NP_116262.2
	UBASH3B	NM_001363365.2		c.53-12660T>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.162-12660T>C		intron	N/A	ENSP00000284273.5
	UBASH3B	ENST00000526386.5	TSL:4	n.214-12660T>C		intron	N/A
	ENSG00000285909	ENST00000649590.1		n.525+739A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22889 AN: 151998 Hom.: 1974 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.151 AC: 22902 AN: 152116 Hom.: 1980 Cov.: 32 AF XY: 0.152 AC XY: 11339 AN XY: 74398

African (AFR) AF: 0.0834 AC: 3462 AN: 41506

American (AMR) AF: 0.205 AC: 3139 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1048 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1226 AN: 5162

South Asian (SAS) AF: 0.207 AC: 997 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1298 AN: 10594

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11018 AN: 67962

Other (OTH) AF: 0.177 AC: 374 AN: 2112

Alfa AF: 0.165 Hom.: 8898

Bravo AF: 0.155

Asia WGS AF: 0.250 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.90
PhyloP100		0.70
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: rs12804711; hg19: chr11-122634267;