rs7112568

Positions:

• chr11-122772249-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.162-3970C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 152,258 control chromosomes in the GnomAD database, including 69,884 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 0.96 (69884 hom., cov: 32)
• Consequence: UBASH3B NM_032873.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBASH3B	NM_032873.5	c.162-3970C>G		intron_variant		ENST00000284273.6	NP_116262.2
UBASH3B	XM_005271712.4	c.-1770C>G		5_prime_UTR_variant	1/14		XP_005271769.1
UBASH3B	NM_001363365.2	c.53-3970C>G		intron_variant			NP_001350294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBASH3B	ENST00000284273.6	c.162-3970C>G		intron_variant		1	NM_032873.5	ENSP00000284273	P1
	ENST00000649590.1	n.74-6200G>C		intron_variant, non_coding_transcript_variant
UBASH3B	ENST00000526386.5	n.214-3970C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145563 AN: 152140 Hom.: 69854 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.980

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.957 AC: 145648 AN: 152258 Hom.: 69884 Cov.: 32 AF XY: 0.955 AC XY: 71107 AN XY: 74444

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.948

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.966

Alfa AF: 0.966 Hom.: 8811

Bravo AF: 0.952

Asia WGS AF: 0.830 AC: 2889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.79
DANN	Benign	0.37

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: rs7112568; hg19: chr11-122642957;