11-122773121-G-T

Variant names:

• chr11-122773121-G-T
• rs4935812
• NM_032873.5:c.162-3098G>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.162-3098G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 152,346 control chromosomes in the GnomAD database, including 70,619 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 (70619 hom., cov: 33)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBASH3B	NM_032873.5	c.162-3098G>T		intron_variant	Intron 1 of 13	ENST00000284273.6	NP_116262.2
UBASH3B	XM_005271712.4	c.-898G>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 14		XP_005271769.1
UBASH3B	XM_005271712.4	c.-898G>T		5_prime_UTR_variant	Exon 1 of 14		XP_005271769.1
UBASH3B	NM_001363365.2	c.53-3098G>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.162-3098G>T		intron_variant	Intron 1 of 13	1	NM_032873.5	ENSP00000284273.5
UBASH3B	ENST00000526386.5	n.214-3098G>T		intron_variant	Intron 1 of 3	4
ENSG00000285909	ENST00000649590.1	n.74-7072C>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146332 AN: 152228 Hom.: 70571 Cov.: 33

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.980

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.970

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

GnomAD4 genome AF: 0.961 AC: 146436 AN: 152346 Hom.: 70619 Cov.: 33 AF XY: 0.960 AC XY: 71493 AN XY: 74504

African (AFR) AF: 0.979 AC: 40694 AN: 41584

American (AMR) AF: 0.948 AC: 14511 AN: 15306

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

East Asian (EAS) AF: 0.689 AC: 3556 AN: 5162

South Asian (SAS) AF: 0.904 AC: 4364 AN: 4830

European-Finnish (FIN) AF: 0.980 AC: 10413 AN: 10628

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

European-Non Finnish (NFE) AF: 0.974 AC: 66251 AN: 68044

Other (OTH) AF: 0.968 AC: 2047 AN: 2114

Alfa AF: 0.969 Hom.: 28116

Bravo AF: 0.961

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.0060
DANN	Benign	0.53
PhyloP100		-2.4
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: rs4935812; hg19: chr11-122643829; COSMIC: COSV52500890; COSMIC: COSV52500890;