rs876498

Variant names:

• chr21-42421718-G-A
• rs876498
• NM_018961.4:c.1046+3109G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018961.4(UBASH3A):​c.1046+3109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,056 control chromosomes in the GnomAD database, including 14,292 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 0.43 (14292 hom., cov: 33)
• Consequence: UBASH3A NM_018961.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 12 publications found

Genes affected

UBASH3A (HGNC:12462): (ubiquitin associated and SH3 domain containing A) This gene encodes one of two family members belonging to the T-cell ubiquitin ligand (TULA) family. Both family members can negatively regulate T-cell signaling. This family member can facilitate growth factor withdrawal-induced apoptosis in T cells, which may occur via its interaction with AIF, an apoptosis-inducing factor. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBASH3A	NM_018961.4	c.1046+3109G>A		intron_variant	Intron 7 of 14	ENST00000319294.11	NP_061834.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBASH3A	ENST00000319294.11	c.1046+3109G>A		intron_variant	Intron 7 of 14	1	NM_018961.4	ENSP00000317327.6

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64888 AN: 151938 Hom.: 14274 Cov.: 33

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.427 AC: 64953 AN: 152056 Hom.: 14292 Cov.: 33 AF XY: 0.417 AC XY: 30978 AN XY: 74318

African (AFR) AF: 0.510 AC: 21152 AN: 41450

American (AMR) AF: 0.374 AC: 5719 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1677 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1623 AN: 5180

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4824

European-Finnish (FIN) AF: 0.312 AC: 3297 AN: 10556

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28586 AN: 67962

Other (OTH) AF: 0.434 AC: 918 AN: 2114

Alfa AF: 0.426 Hom.: 5688

Bravo AF: 0.436

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.49
PhyloP100		-1.3
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: rs876498; hg19: chr21-43841827;