rs4935804

chr11-122735201-A-Gchr11-122735201-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
UBASH3B	NM_032873.5	c.162-41018A>G		intron_variant		ENST00000284273.6
UBASH3B	NM_001363365.2	c.53-41018A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBASH3B	ENST00000284273.6	c.162-41018A>G		intron_variant		1	NM_032873.5	P1
UBASH3B	ENST00000526386.5	n.213+25727A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.373

Alfa AF: 0.405 Hom.: 7169

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs4935804; hg19: chr11-122605909;