NM_032873.5:c.162-3970C>G

Variant names:

• chr11-122772249-C-G
• rs7112568
• NM_032873.5:c.162-3970C>G

Variant summary

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

The NM_032873.5(UBASH3B):​c.162-3970C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 152,258 control chromosomes in the GnomAD database, including 69,884 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 0.96 (69884 hom., cov: 32)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBASH3B	NM_032873.5	MANE Select	c.162-3970C>G		intron	N/A	NP_116262.2
	UBASH3B	NM_001363365.2		c.53-3970C>G		intron	N/A	NP_001350294.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBASH3B	ENST00000284273.6	TSL:1 MANE Select	c.162-3970C>G		intron	N/A	ENSP00000284273.5	Q8TF42
	UBASH3B	ENST00000526386.5	TSL:4	n.214-3970C>G		intron	N/A
	ENSG00000285909	ENST00000649590.1		n.74-6200G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145563 AN: 152140 Hom.: 69854 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.980

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.957 AC: 145648 AN: 152258 Hom.: 69884 Cov.: 32 AF XY: 0.955 AC XY: 71107 AN XY: 74444

African (AFR) AF: 0.960 AC: 39893 AN: 41550

American (AMR) AF: 0.948 AC: 14505 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3412 AN: 3472

East Asian (EAS) AF: 0.699 AC: 3605 AN: 5160

South Asian (SAS) AF: 0.909 AC: 4381 AN: 4822

European-Finnish (FIN) AF: 0.980 AC: 10395 AN: 10608

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66224 AN: 68024

Other (OTH) AF: 0.966 AC: 2045 AN: 2116

Alfa AF: 0.966 Hom.: 8811

Bravo AF: 0.952

Asia WGS AF: 0.830 AC: 2889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.79
DANN	Benign	0.37
PhyloP100		-0.36
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: rs7112568; hg19: chr11-122642957;