rs4935804

Variant names:

• chr11-122735201-A-G
• rs4935804
• NM_032873.5:c.162-41018A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-122735201-A-G
• chr11-122735201-A-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.162-41018A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,116 control chromosomes in the GnomAD database, including 9,088 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 0.32 (9088 hom., cov: 32)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 4 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBASH3B	NM_032873.5	c.162-41018A>G		intron_variant	Intron 1 of 13	ENST00000284273.6	NP_116262.2
UBASH3B	NM_001363365.2	c.53-41018A>G		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.162-41018A>G		intron_variant	Intron 1 of 13	1	NM_032873.5	ENSP00000284273.5
UBASH3B	ENST00000526386.5	n.213+25727A>G		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48011 AN: 151998 Hom.: 9091 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.316 AC: 48010 AN: 152116 Hom.: 9088 Cov.: 32 AF XY: 0.312 AC XY: 23190 AN XY: 74364

African (AFR) AF: 0.111 AC: 4625 AN: 41516

American (AMR) AF: 0.288 AC: 4399 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1750 AN: 3470

East Asian (EAS) AF: 0.141 AC: 728 AN: 5178

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4820

European-Finnish (FIN) AF: 0.368 AC: 3884 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29451 AN: 67982

Other (OTH) AF: 0.373 AC: 790 AN: 2116

Alfa AF: 0.395 Hom.: 11388

Bravo AF: 0.298

Asia WGS AF: 0.264 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.80
PhyloP100		-0.92
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: rs4935804; hg19: chr11-122605909;