11-122709411-G-T

Variant names:

• chr11-122709411-G-T
• rs10790521
• NM_032873.5:c.161+53201G>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.161+53201G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,066 control chromosomes in the GnomAD database, including 8,373 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 0.31 (8373 hom., cov: 32)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.76
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032873.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBASH3B	NM_032873.5	MANE Select	c.161+53201G>T		intron	N/A	NP_116262.2
	UBASH3B	NM_001363365.2		c.52+53201G>T		intron	N/A	NP_001350294.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBASH3B	ENST00000284273.6	TSL:1 MANE Select	c.161+53201G>T		intron	N/A	ENSP00000284273.5
	UBASH3B	ENST00000526386.5	TSL:4	n.150G>T		non_coding_transcript_exon	Exon 1 of 4
	UBASH3B	ENST00000525711.1	TSL:4	n.487-18103G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47367 AN: 151938 Hom.: 8356 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.300 AC: 3 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.312 AC: 47392 AN: 152056 Hom.: 8373 Cov.: 32 AF XY: 0.323 AC XY: 23977 AN XY: 74310

African (AFR) AF: 0.170 AC: 7063 AN: 41498

American (AMR) AF: 0.420 AC: 6411 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3472

East Asian (EAS) AF: 0.680 AC: 3511 AN: 5160

South Asian (SAS) AF: 0.425 AC: 2047 AN: 4818

European-Finnish (FIN) AF: 0.386 AC: 4070 AN: 10540

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21590 AN: 67988

Other (OTH) AF: 0.338 AC: 713 AN: 2110

Alfa AF: 0.315 Hom.: 19938

Bravo AF: 0.311

Asia WGS AF: 0.480 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.7
DANN	Benign	0.69
PhyloP100		2.8
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: rs10790521; hg19: chr11-122580119;