rs12804711

chr11-122763559-T-C

Variant summary

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

The NM_032873.5(UBASH3B):c.162-12660T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,116 control chromosomes in the GnomAD database, including 1,980 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 0.15 (1980 hom., cov: 32)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBASH3B	NM_032873.5	c.162-12660T>C		intron_variant		ENST00000284273.6
UBASH3B	NM_001363365.2	c.53-12660T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBASH3B	ENST00000284273.6	c.162-12660T>C		intron_variant		1	NM_032873.5	P1
	ENST00000649590.1	n.525+739A>G		intron_variant, non_coding_transcript_variant
UBASH3B	ENST00000526386.5	n.214-12660T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22889 AN: 151998 Hom.: 1974 Cov.: 32

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.151 AC: 22902 AN: 152116 Hom.: 1980 Cov.: 32 AF XY: 0.152 AC XY: 11339 AN XY: 74398

Gnomad4 AFR AF: 0.0834

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.177

Alfa AF: 0.172 Hom.: 4382

Bravo AF: 0.155

Asia WGS AF: 0.250 AC: 867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	11
Dann	Benign	0.90

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: rs12804711; hg19: chr11-122634267;