11-122659883-C-G

Position:

• chr11-122659883-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032873.5(UBASH3B):​c.161+3673C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,772 control chromosomes in the GnomAD database, including 11,574 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 0.39 (11574 hom., cov: 31)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBASH3B	NM_032873.5	c.161+3673C>G		intron_variant		ENST00000284273.6
UBASH3B	NM_001363365.2	c.52+3673C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBASH3B	ENST00000284273.6	c.161+3673C>G		intron_variant		1	NM_032873.5	P1
UBASH3B	ENST00000525711.1	n.486+3673C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58692 AN: 151654 Hom.: 11543 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.387 AC: 58770 AN: 151772 Hom.: 11574 Cov.: 31 AF XY: 0.383 AC XY: 28379 AN XY: 74138

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.385

Alfa AF: 0.406 Hom.: 1577

Bravo AF: 0.386

Asia WGS AF: 0.388 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.69

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: rs7115089; hg19: chr11-122530591;