11-122770378-T-C

Variant names:

• chr11-122770378-T-C
• rs4936742
• NM_032873.5:c.162-5841T>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.162-5841T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,836 control chromosomes in the GnomAD database, including 31,493 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 0.63 (31493 hom., cov: 31)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 12 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBASH3B	NM_032873.5	c.162-5841T>C		intron_variant	Intron 1 of 13	ENST00000284273.6	NP_116262.2
UBASH3B	XM_005271712.4	c.-3641T>C		5_prime_UTR_variant	Exon 1 of 14		XP_005271769.1
UBASH3B	NM_001363365.2	c.53-5841T>C		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.162-5841T>C		intron_variant	Intron 1 of 13	1	NM_032873.5	ENSP00000284273.5
UBASH3B	ENST00000526386.5	n.214-5841T>C		intron_variant	Intron 1 of 3	4
ENSG00000285909	ENST00000649590.1	n.74-4329A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96174 AN: 151720 Hom.: 31464 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.634 AC: 96262 AN: 151836 Hom.: 31493 Cov.: 31 AF XY: 0.636 AC XY: 47161 AN XY: 74180

African (AFR) AF: 0.798 AC: 33036 AN: 41418

American (AMR) AF: 0.588 AC: 8971 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1541 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2173 AN: 5146

South Asian (SAS) AF: 0.538 AC: 2590 AN: 4816

European-Finnish (FIN) AF: 0.673 AC: 7047 AN: 10474

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39055 AN: 67936

Other (OTH) AF: 0.585 AC: 1235 AN: 2110

Alfa AF: 0.581 Hom.: 44430

Bravo AF: 0.634

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.37
PhyloP100		-1.2
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: rs4936742; hg19: chr11-122641086;